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3
404.html
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@ -30,7 +30,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -46,6 +46,7 @@
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="https://msberends.github.io/AMR/articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
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@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

64
articles/AMR.html
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@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -87,7 +88,7 @@
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 15 December 2024.</p>
generated on 19 December 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -143,21 +144,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-12-15</td>
<td align="center">2024-12-19</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">2024-12-15</td>
<td align="center">2024-12-19</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">2024-12-15</td>
<td align="center">2024-12-19</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -176,8 +177,11 @@ creating beautiful plots in R.</p>
<p>We will also use the <code>cleaner</code> package, that can be used
for cleaning data and creating frequency tables.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></code></pre></div>
<p>Error in get(paste0(generic, “.”, class), envir = get_method_env()) :
object ‘type_sum.accel’ not found</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># (if not yet installed, install with:)</span></span>
@ -185,7 +189,7 @@ for cleaning data and creating frequency tables.</p>
<p>The <code>AMR</code> package contains a data set
<code>example_isolates_unclean</code>, which might look data that users
have extracted from their laboratory systems:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates_unclean</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
@ -218,7 +222,7 @@ included data were retrieved on 24 Jun 2024.</p>
<p>The codes of the AMR packages that come from <code><a href="../reference/as.mo.html">as.mo()</a></code> are
short, but still human readable. More importantly, <code><a href="../reference/as.mo.html">as.mo()</a></code>
supports all kinds of input:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
@ -238,7 +242,7 @@ retrieve taxonomic properties, such as the name, genus, species, family,
order, and even Gram-stain. They all start with <code>mo_</code> and
they use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally, so that still any arbitrary
user input can be used:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Enterobacteriaceae"</span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
@ -257,14 +261,14 @@ user input can be used:</p>
<span><span class="co">#&gt; [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span></span>
<span><span class="co">#&gt; [5] "56415008" "714315002" "713926009"</span></span></code></pre></div>
<p>Now we can thus clean our data:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span>
<span><span class="co">#&gt; mo_uncertainties() to review these uncertainties, or use</span></span>
<span><span class="co">#&gt; add_custom_microorganisms() to add custom entries.</span></span></code></pre></div>
<p>Apparently, there was some uncertainty about the translation to
taxonomic codes. Let’s check this:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; Matching scores are based on the resemblance between the input and the full</span></span>
<span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
@ -321,10 +325,10 @@ diffusion values, read more about that on the <code><a href="../reference/as.sir
page.</p>
<p>For now, we will just clean the SIR columns in our data using
dplyr:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># method 1, be explicit about the columns:</span></span>
<span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># method 2, let the AMR package determine the eligible columns</span></span>
<span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -389,7 +393,7 @@ analysis, but the default phenotype-based method is in any case the
method to properly correct for most duplicate isolates. Read more about
the methods on the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> page.</p>
<p>The outcome of the function can easily be added to our data:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Determining first isolates using an episode length of 365 days</span></span>
@ -403,16 +407,16 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<p>So only 91% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p>For future use, the above two syntaxes can be shortened:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 2 724 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@ -437,7 +441,7 @@ like:</p>
<p>The base R <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function gives a good first
impression, as it comes with support for the new <code>mo</code> and
<code>sir</code> classes that we now have in our data set:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; patient_id hospital date </span></span>
<span><span class="co">#&gt; Length:2724 Length:2724 Min. :2011-01-01 </span></span>
@ -486,7 +490,7 @@ impression, as it comes with support for the new <code>mo</code> and
<p>To just get an idea how the species are distributed, create a
frequency table with <code><a href="../reference/count.html">count()</a></code> based on the name of the
microorganisms:</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
@ -513,7 +517,7 @@ microorganisms:</p>
<p>Using so-called antibiotic class selectors, you can select or filter
columns based on the antibiotic class that your antibiotic results are
in:</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
@ -658,7 +662,7 @@ failure</li>
function to create any of the above antibiogram types. For starters,
this is what the included <code>example_isolates</code> data set looks
like:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
@ -687,7 +691,7 @@ like:</p>
should be used. The <code>antibiotics</code> argument in the
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports any (combination) of the
previously mentioned antibiotic class selectors:</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ The function aminoglycosides() should be used inside a dplyr verb or</span></span>
@ -831,7 +835,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
Swedish, Turkish, or Ukrainian. In this next example, we force the
language to be Spanish using the <code>language</code> argument:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
@ -885,7 +889,7 @@ language to be Spanish using the <code>language</code> argument:</p>
</h4>
<p>To create a combined antibiogram, use antibiotic codes or names with
a plus <code>+</code> character like this:</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
@ -965,7 +969,7 @@ a plus <code>+</code> character like this:</p>
<p>To create a syndromic antibiogram, the <code>syndromic_group</code>
argument must be used. This can be any column in the data, or e.g. an
<code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
@ -1165,7 +1169,7 @@ Antibiogram) in which cases are predefined based on clinical or
demographic characteristics (e.g., endocarditis in 75+ females). This
next example is a simplification without clinical characteristics, but
just gives an idea of how a WISCA can be created:</p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">wisca</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
@ -1233,7 +1237,7 @@ just gives an idea of how a WISCA can be created:</p>
<p>Antibiograms can be plotted using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> from the
<code>ggplot2</code> packages, since this <code>AMR</code> package
provides an extension to that function:</p>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">wisca</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_files/figure-html/unnamed-chunk-10-1.png" width="720"></p>
<p>To calculate antimicrobial resistance in a more sensible way, also by
@ -1262,12 +1266,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to
<code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their
own:</p>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span><span class="op">)</span></span>

3
articles/AMR_for_Python.html
View File

@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

403
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@ -0,0 +1,403 @@
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<img src="../logo.svg" class="logo" alt=""><h1>`AMR` with `tidymodels`</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR_with_tidymodels.Rmd" class="external-link"><code>vignettes/AMR_with_tidymodels.Rmd</code></a></small>
<div class="d-none name"><code>AMR_with_tidymodels.Rmd</code></div>
</div>
<p>Antimicrobial resistance (AMR) is a global health crisis, and
understanding resistance patterns is crucial for managing effective
treatments. The <code>AMR</code> R package provides robust tools for
analysing AMR data, including convenient antibiotic selector functions
like <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>. In
this post, we will explore how to use the <code>tidymodels</code>
framework to predict resistance patterns in the
<code>example_isolates</code> dataset.</p>
<p>By leveraging the power of <code>tidymodels</code> and the
<code>AMR</code> package, we’ll build a reproducible machine learning
workflow to predict resistance to two important antibiotic classes:
aminoglycosides and beta-lactams.</p>
<hr>
<div class="section level3">
<h3 id="objective">
<strong>Objective</strong><a class="anchor" aria-label="anchor" href="#objective"></a>
</h3>
<p>Our goal is to build a predictive model using the
<code>tidymodels</code> framework to determine resistance patterns based
on microbial data. We will:</p>
<ol style="list-style-type: decimal">
<li>Preprocess data using the selector functions
<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>.</li>
<li>Define a logistic regression model for prediction.</li>
<li>Use a structured <code>tidymodels</code> workflow to preprocess,
train, and evaluate the model.</li>
</ol>
<hr>
</div>
<div class="section level3">
<h3 id="data-preparation">
<strong>Data Preparation</strong><a class="anchor" aria-label="anchor" href="#data-preparation"></a>
</h3>
<p>We begin by loading the required libraries and preparing the
<code>example_isolates</code> dataset from the <code>AMR</code>
package.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span>
<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
<span><span class="co">#&gt; object 'type_sum.accel' not found</span></span>
<span><span class="co">#&gt; ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.2.0 ──</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.7 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.1.0</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.3.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dplyr </span> 1.1.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">ggplot2 </span> 3.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.7 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.1.4</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.2.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.0</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.0.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.1</span></span>
<span><span class="co">#&gt; ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span> masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span> masks <span style="color: #0000BB;">stats</span>::step()</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Use <span style="color: #00BB00;">tidymodels_prefer()</span> to resolve common conflicts.</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
<span></span>
<span><span class="co"># Load the example_isolates dataset</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"example_isolates"</span><span class="op">)</span> <span class="co"># Preloaded dataset with AMR results</span></span>
<span></span>
<span><span class="co"># Select relevant columns for prediction</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># select AB results dynamically</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># replace NAs with NI (not-interpretable)</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
<span> <span class="op">~</span><span class="fu">replace_na</span><span class="op">(</span><span class="va">.x</span>, <span class="st">"NI"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="co"># make factors of SIR columns</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
<span> <span class="va">as.integer</span><span class="op">)</span>,</span>
<span> <span class="co"># get Gramstain of microorganisms</span></span>
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span> <span class="co"># %&gt;%</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
<span><span class="co">#&gt; (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
<span><span class="co">#&gt; (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
<span><span class="co">#&gt; 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span>
<span> <span class="co"># Cefepime is not reliable</span></span>
<span> <span class="co">#select(-FEP)</span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
<code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> dynamically select columns for antibiotics in
these classes. - <code>drop_na()</code> ensures the model receives
complete cases for training.</p>
<hr>
</div>
<div class="section level3">
<h3 id="defining-the-workflow">
<strong>Defining the Workflow</strong><a class="anchor" aria-label="anchor" href="#defining-the-workflow"></a>
</h3>
<p>We now define the <code>tidymodels</code> workflow, which consists of
three steps: preprocessing, model specification, and fitting.</p>
<div class="section level4">
<h4 id="preprocessing-with-a-recipe">1. Preprocessing with a Recipe<a class="anchor" aria-label="anchor" href="#preprocessing-with-a-recipe"></a>
</h4>
<p>We create a recipe to preprocess the data for modelling. This
includes: - Encoding resistance results (<code>S</code>, <code>I</code>,
<code>R</code>) as binary (resistant or not resistant). - Converting
microbial organism names (<code>mo</code>) into numerical features using
one-hot encoding.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Define the recipe for data preprocessing</span></span>
<span><span class="va">resistance_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">mo</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">data</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">step_corr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span>
<span><span class="va">resistance_recipe</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Inputs</span></span>
<span><span class="co">#&gt; Number of variables by role</span></span>
<span><span class="co">#&gt; outcome: 1</span></span>
<span><span class="co">#&gt; predictor: 20</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Operations</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Correlation filter on: <span style="color: #0000BB;">c(aminoglycosides(), betalactams())</span></span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>step_mutate()</code> transforms
resistance results (<code>R</code>) into binary variables (TRUE/FALSE).
- <code>step_dummy()</code> converts categorical organism
(<code>mo</code>) names into one-hot encoded numerical features, making
them compatible with the model.</p>
</div>
<div class="section level4">
<h4 id="specifying-the-model">2. Specifying the Model<a class="anchor" aria-label="anchor" href="#specifying-the-model"></a>
</h4>
<p>We define a logistic regression model since resistance prediction is
a binary classification task.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Specify a logistic regression model</span></span>
<span><span class="va">logistic_model</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">set_engine</span><span class="op">(</span><span class="st">"glm"</span><span class="op">)</span> <span class="co"># Use the Generalized Linear Model engine</span></span>
<span><span class="va">logistic_model</span></span>
<span><span class="co">#&gt; Logistic Regression Model Specification (classification)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Computational engine: glm</span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>logistic_reg()</code> sets up a
logistic regression model. - <code>set_engine("glm")</code> specifies
the use of R’s built-in GLM engine.</p>
</div>
<div class="section level4">
<h4 id="building-the-workflow">3. Building the Workflow<a class="anchor" aria-label="anchor" href="#building-the-workflow"></a>
</h4>
<p>We bundle the recipe and model together into a <code>workflow</code>,
which organizes the entire modeling process.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Combine the recipe and model into a workflow</span></span>
<span><span class="va">resistance_workflow</span> <span class="op">&lt;-</span> <span class="fu">workflow</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">add_recipe</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Add the preprocessing recipe</span></span>
<span> <span class="fu">add_model</span><span class="op">(</span><span class="va">logistic_model</span><span class="op">)</span> <span class="co"># Add the logistic regression model</span></span>
<span><span class="va">resistance_workflow</span></span>
<span><span class="co">#&gt; ══ Workflow ════════════════════════════════════════════════════════════════════</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Preprocessor:</span> Recipe</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Model:</span> logistic_reg()</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Preprocessor ────────────────────────────────────────────────────────────────</span></span>
<span><span class="co">#&gt; 1 Recipe Step</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; • step_corr()</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Model ───────────────────────────────────────────────────────────────────────</span></span>
<span><span class="co">#&gt; Logistic Regression Model Specification (classification)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Computational engine: glm</span></span></code></pre></div>
<hr>
</div>
</div>
<div class="section level3">
<h3 id="training-and-evaluating-the-model">
<strong>Training and Evaluating the Model</strong><a class="anchor" aria-label="anchor" href="#training-and-evaluating-the-model"></a>
</h3>
<p>To train the model, we split the data into training and testing sets.
Then, we fit the workflow on the training set and evaluate its
performance.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Split data into training and testing sets</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span> <span class="co"># For reproducibility</span></span>
<span><span class="va">data_split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span>, prop <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span> <span class="co"># 80% training, 20% testing</span></span>
<span><span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span> <span class="co"># Training set</span></span>
<span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">data_split</span><span class="op">)</span> <span class="co"># Testing set</span></span>
<span></span>
<span><span class="co"># Fit the workflow to the training data</span></span>
<span><span class="va">fitted_workflow</span> <span class="op">&lt;-</span> <span class="va">resistance_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">fit</span><span class="op">(</span><span class="va">training_data</span><span class="op">)</span> <span class="co"># Train the model</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
<span><span class="co">#&gt; (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
<span><span class="co">#&gt; (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
<span><span class="co">#&gt; 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span>
<span></span>
<span><span class="va">fitted_workflow</span></span>
<span><span class="co">#&gt; ══ Workflow [trained] ══════════════════════════════════════════════════════════</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Preprocessor:</span> Recipe</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Model:</span> logistic_reg()</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Preprocessor ────────────────────────────────────────────────────────────────</span></span>
<span><span class="co">#&gt; 1 Recipe Step</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; • step_corr()</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; ── Model ───────────────────────────────────────────────────────────────────────</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Call: stats::glm(formula = ..y ~ ., family = stats::binomial, data = data)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Coefficients:</span></span>
<span><span class="co">#&gt; (Intercept) GEN TOB AMK KAN PEN </span></span>
<span><span class="co">#&gt; 101.11641 -3.69738 4.55879 1.86703 -23.37497 -0.57182 </span></span>
<span><span class="co">#&gt; OXA FLC AMC AMP TZP CZO </span></span>
<span><span class="co">#&gt; -4.68575 -11.69742 0.79748 -1.56197 0.87667 -2.28424 </span></span>
<span><span class="co">#&gt; FEP CXM FOX CAZ CRO IPM </span></span>
<span><span class="co">#&gt; -0.19847 0.02659 10.32455 10.27248 0.97321 -0.93096 </span></span>
<span><span class="co">#&gt; MEM </span></span>
<span><span class="co">#&gt; -0.88753 </span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Degrees of Freedom: 1573 Total (i.e. Null); 1555 Residual</span></span>
<span><span class="co">#&gt; Null Deviance: 2071 </span></span>
<span><span class="co">#&gt; Residual Deviance: 74.91 AIC: 112.9</span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>initial_split()</code> splits
the data into training and testing sets. - <code>fit()</code> trains the
workflow on the training set.</p>
<p>Next, we evaluate the model on the testing data.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Make predictions on the testing set</span></span>
<span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span><span class="op">)</span> <span class="co"># Generate predictions</span></span>
<span><span class="va">probabilities</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span>, type <span class="op">=</span> <span class="st">"prob"</span><span class="op">)</span> <span class="co"># Generate probabilities</span></span>
<span></span>
<span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">probabilities</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">testing_data</span><span class="op">)</span> <span class="co"># Combine with true labels</span></span>
<span></span>
<span><span class="va">predictions</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 394 × 24</span></span></span>
<span><span class="co">#&gt; .pred_class `.pred_Gram-negative` `.pred_Gram-positive` mo GEN TOB</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive 3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span> 1.00<span style="color: #949494;">e</span>+ 0 Gram-p… 5 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative 9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 1.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative 9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 5.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 1 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative 1 <span style="color: #949494;">e</span>+ 0 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n… 1 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive 6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span> 1.00<span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 384 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 18 more variables: AMK &lt;int&gt;, KAN &lt;int&gt;, PEN &lt;int&gt;, OXA &lt;int&gt;, FLC &lt;int&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># AMX &lt;int&gt;, AMC &lt;int&gt;, AMP &lt;int&gt;, TZP &lt;int&gt;, CZO &lt;int&gt;, FEP &lt;int&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;int&gt;, FOX &lt;int&gt;, CTX &lt;int&gt;, CAZ &lt;int&gt;, CRO &lt;int&gt;, IPM &lt;int&gt;, MEM &lt;int&gt;</span></span></span>
<span></span>
<span><span class="co"># Evaluate model performance</span></span>
<span><span class="va">metrics</span> <span class="op">&lt;-</span> <span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">metrics</span><span class="op">(</span>truth <span class="op">=</span> <span class="va">mo</span>, estimate <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span> <span class="co"># Calculate performance metrics</span></span>
<span></span>
<span><span class="va">metrics</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 3</span></span></span>
<span><span class="co">#&gt; .metric .estimator .estimate</span></span>
<span><span class="co">#&gt; <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;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> accuracy binary 0.995</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> kap binary 0.989</span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict()</a></code> generates
predictions on the testing set. - <code>metrics()</code> computes
evaluation metrics like accuracy and AUC.</p>
<p>It appears we can predict the Gram based on AMR results with a 0.995
accuracy. The ROC curve looks like:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">roc_curve</span><span class="op">(</span><span class="va">mo</span>, <span class="va">`.pred_Gram-negative`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<hr>
</div>
<div class="section level3">
<h3 id="conclusion">
<strong>Conclusion</strong><a class="anchor" aria-label="anchor" href="#conclusion"></a>
</h3>
<p>In this post, we demonstrated how to build a machine learning
pipeline with the <code>tidymodels</code> framework and the
<code>AMR</code> package. By combining selector functions like
<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> with
<code>tidymodels</code>, we efficiently prepared data, trained a model,
and evaluated its performance.</p>
<p>This workflow is extensible to other antibiotic classes and
resistance patterns, empowering users to analyse AMR data systematically
and reproducibly.</p>
<hr>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
</div>
<footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
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@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
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@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

79
articles/PCA.html
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@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -96,6 +97,8 @@ is currently being developed.</strong></p>
<code>example_isolates</code> data set in this package looks like:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
<span><span class="co">#&gt; object 'type_sum.accel' not found</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,000</span></span>
@ -107,45 +110,45 @@ is currently being developed.</strong></p>
<span><span class="co">#&gt; $ ward <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…</span></span>
<span><span class="co">#&gt; $ mo <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…</span></span>
<span><span class="co">#&gt; $ PEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co">#&gt; $ OXA <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ FLC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
<span><span class="co">#&gt; $ AMX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co">#&gt; $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
<span><span class="co">#&gt; $ AMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
<span><span class="co">#&gt; $ TZP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ CZO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co">#&gt; $ FEP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ CXM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
<span><span class="co">#&gt; $ FOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
<span><span class="co">#&gt; $ CTX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co">#&gt; $ CAZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
<span><span class="co">#&gt; $ CRO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co">#&gt; $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ TOB <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ AMK <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ KAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ TMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
<span><span class="co">#&gt; $ SXT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
<span><span class="co">#&gt; $ NIT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
<span><span class="co">#&gt; $ FOS <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ LNZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co">#&gt; $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
<span><span class="co">#&gt; $ MFX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ VAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
<span><span class="co">#&gt; $ TEC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
<span><span class="co">#&gt; $ TCY <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
<span><span class="co">#&gt; $ TGC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co">#&gt; $ DOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
<span><span class="co">#&gt; $ OXA <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ FLC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, S, S, R, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R…</span></span>
<span><span class="co">#&gt; $ AMX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, I, I, R, I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ AMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ TZP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ CZO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
<span><span class="co">#&gt; $ FEP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ CXM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, R, R, S, S…</span></span>
<span><span class="co">#&gt; $ FOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
<span><span class="co">#&gt; $ CTX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
<span><span class="co">#&gt; $ CAZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, R, R, …</span></span>
<span><span class="co">#&gt; $ CRO <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
<span><span class="co">#&gt; $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ TOB <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ AMK <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ KAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ TMP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, R, R, R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, R, R, R, …</span></span>
<span><span class="co">#&gt; $ SXT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ NIT <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R,…</span></span>
<span><span class="co">#&gt; $ FOS <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ LNZ <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
<span><span class="co">#&gt; $ MFX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ VAN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, S, S, S, …</span></span>
<span><span class="co">#&gt; $ TEC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
<span><span class="co">#&gt; $ TCY <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, S, S, S, S, S, S, S, I, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, I, R, R, S, I, R, …</span></span>
<span><span class="co">#&gt; $ TGC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ DOX <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ ERY <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co">#&gt; $ CLI <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
<span><span class="co">#&gt; $ CLI <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ AZM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
<span><span class="co">#&gt; $ IPM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
<span><span class="co">#&gt; $ MEM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ MTR <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ CHL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ COL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
<span><span class="co">#&gt; $ MUP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
<span><span class="co">#&gt; $ RIF <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
<span><span class="co">#&gt; $ IPM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
<span><span class="co">#&gt; $ MEM <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ MTR <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ CHL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ COL <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, …</span></span>
<span><span class="co">#&gt; $ MUP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
<span><span class="co">#&gt; $ RIF <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span></code></pre></div>
<p>Now to transform this to a data set with only resistance percentages
per taxonomic order and genus:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">

5
articles/WHONET.html
View File

@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -107,6 +108,8 @@ the tidyverse for all of my analyses. All of them. If you don’t know it
yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
<span><span class="co">#&gt; object 'type_sum.accel' not found</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/cleaner/" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>

5
articles/datasets.html
View File

@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -76,7 +77,7 @@
<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">15 December 2024</h4>
<h4 data-toc-skip class="date">19 December 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

5
articles/index.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -50,6 +51,8 @@
<div class="section-desc"></div>
<dl><dt><a href="AMR_for_Python.html">AMR for Python</a></dt>
<dd>
</dd><dt><a href="AMR_with_tidymodels.html">`AMR` with `tidymodels`</a></dt>
<dd>
</dd><dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
<dd>

5
articles/resistance_predict.html
View File

@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -95,6 +96,8 @@ plots in R.</p>
extends their use and functions.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
<span><span class="co">#&gt; object 'type_sum.accel' not found</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span></span>

3
articles/welcome_to_AMR.html
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@ -29,7 +29,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -45,6 +45,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
authors.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
index.html
View File

@ -32,7 +32,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -48,6 +48,7 @@
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

26
news/index.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -47,18 +48,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9120" id="amr-2119120">AMR 2.1.1.9120<a class="anchor" aria-label="anchor" href="#amr-2119120"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9121" id="amr-2119121">AMR 2.1.1.9121<a class="anchor" aria-label="anchor" href="#amr-2119121"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9120">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9120"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9121">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9121"></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’s Atlantic Veterinary College</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-2-1-1-9120">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9120"></a></h3>
<h3 id="breaking-2-1-1-9121">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9121"></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-2-1-1-9120">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9120"></a></h3>
<h3 id="new-2-1-1-9121">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9121"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary 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>
@ -94,12 +95,16 @@
<ul><li>While using R for the heavy lifting, <a href="https://pypi.org/project/AMR/" class="external-link">our ‘AMR’ Python Package</a> was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.</li>
</ul></li>
<li>
<strong>Support for <code>tidymodels</code></strong>
<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using AMR function for predictive modelling.</li>
</ul></li>
<li>
<strong>Other</strong>
<ul><li>New 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 belong to that group.</li>
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9120">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9120"></a></h3>
<h3 id="changed-2-1-1-9121">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9121"></a></h3>
<ul><li>SIR interpretation
<ul><li>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>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -153,17 +158,20 @@
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
<li>
<code><a href="../reference/plot.html">scale_y_percent()</a></code> can now cope with ranges outside the 0-100% range</li>
<li>Support for new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li>
<li>MDRO determination (using <code><a href="../reference/mdro.html">mdro()</a></code>)
<ul><li>Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)</li>
<li>Added arguments <code>esbl</code>, <code>carbapenemase</code>, <code>mecA</code>, <code>mecC</code>, <code>vanA</code>, <code>vanB</code> to denote column names or logical values indicating presence of these genes (or production of their proteins)</li>
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9120">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9120"></a></h3>
<h3 id="other-2-1-1-9121">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9121"></a></h3>
<ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
<li>Greatly updated and expanded documentation</li>
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9120">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9120"></a></h3>
<h3 id="older-versions-2-1-1-9121">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9121"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

3
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View File

@ -3,6 +3,7 @@ pkgdown: 2.1.1
pkgdown_sha: ~
articles:
AMR_for_Python: AMR_for_Python.html
AMR_with_tidymodels: AMR_with_tidymodels.html
AMR: AMR.html
datasets: datasets.html
EUCAST: EUCAST.html
@ -11,7 +12,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-12-15T19:36Z
last_built: 2024-12-19T19:21Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

3
reference/AMR-options.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/AMR.html
View File

@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -35,6 +35,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/WHOCC.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/WHONET.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/ab_from_text.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/ab_property.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/add_custom_antimicrobials.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/add_custom_microorganisms.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

23
reference/age.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -110,16 +111,16 @@
<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 59 59.02732 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.78962 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.12022 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.83333 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.81967 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.92896 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.30055 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.88525 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.49454 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.34699 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.03825 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.80055 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.13115 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.84426 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.83060 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.93989 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.31148 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.89617 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.50546 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.35792 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

3
reference/age_groups.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/antibiogram.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/antibiotic_class_selectors.html
View File

@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/antibiotics.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/as.ab.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/as.av.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/as.disk.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/as.mic.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/as.mo.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

23
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -35,6 +35,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -785,16 +786,16 @@ 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: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-12-15 <span style="color: #949494;">19:37:06</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-12-15 <span style="color: #949494;">19:37:13</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-12-15 <span style="color: #949494;">19:37:13</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-12-15 <span style="color: #949494;">19:37:14</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-12-15 <span style="color: #949494;">19:37:14</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-12-15 <span style="color: #949494;">19:37:06</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-12-15 <span style="color: #949494;">19:37:13</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-12-15 <span style="color: #949494;">19:37:13</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-12-15 <span style="color: #949494;">19:37:14</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-12-15 <span style="color: #949494;">19:37:14</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-12-19 <span style="color: #949494;">19:22:22</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-12-19 <span style="color: #949494;">19:22:29</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-12-19 <span style="color: #949494;">19:22:29</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-12-19 <span style="color: #949494;">19:22:30</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-12-19 <span style="color: #949494;">19:22:30</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-12-19 <span style="color: #949494;">19:22:22</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-12-19 <span style="color: #949494;">19:22:29</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-12-19 <span style="color: #949494;">19:22:29</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-12-19 <span style="color: #949494;">19:22:30</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-12-19 <span style="color: #949494;">19:22:30</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

3
reference/atc_online.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/av_from_text.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/av_property.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/availability.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/bug_drug_combinations.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/clinical_breakpoints.html
View File

@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -35,6 +35,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/custom_eucast_rules.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/dosage.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/eucast_rules.html
View File

@ -9,7 +9,7 @@ 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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/example_isolates.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/example_isolates_unclean.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/export_ncbi_biosample.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/first_isolate.html
View File

@ -9,7 +9,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/g.test.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/get_episode.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/ggplot_pca.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/ggplot_sir.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/guess_ab_col.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/index.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/intrinsic_resistant.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/italicise_taxonomy.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/join.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/key_antimicrobials.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/kurtosis.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/like.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

46
reference/mdro.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
@ -57,6 +58,12 @@
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> guideline <span class="op">=</span> <span class="st">"CMI2012"</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> esbl <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> carbapenemase <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> mecA <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> mecC <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> vanA <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> vanB <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> pct_required_classes <span class="op">=</span> <span class="fl">0.5</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@ -69,13 +76,18 @@
<span></span>
<span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -98,6 +110,30 @@
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-esbl">esbl<a class="anchor" aria-label="anchor" href="#arg-esbl"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins)</p></dd>
<dt id="arg-carbapenemase">carbapenemase<a class="anchor" aria-label="anchor" href="#arg-carbapenemase"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins)</p></dd>
<dt id="arg-meca">mecA<a class="anchor" aria-label="anchor" href="#arg-meca"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecA</em> gene (or production of its proteins)</p></dd>
<dt id="arg-mecc">mecC<a class="anchor" aria-label="anchor" href="#arg-mecc"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecC</em> gene (or production of its proteins)</p></dd>
<dt id="arg-vana">vanA<a class="anchor" aria-label="anchor" href="#arg-vana"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanA</em> gene (or production of its proteins)</p></dd>
<dt id="arg-vanb">vanB<a class="anchor" aria-label="anchor" href="#arg-vanb"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanB</em> gene (or production of its proteins)</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>

3
reference/mean_amr_distance.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/microorganisms.codes.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/microorganisms.groups.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/mo_property.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/mo_source.html
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@ -9,7 +9,7 @@ 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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/pca.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/plot.html
View File

@ -9,7 +9,7 @@ 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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/proportion.html
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@ -9,7 +9,7 @@ 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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/random.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/resistance_predict.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/skewness.html
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@ -9,7 +9,7 @@ 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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -23,6 +23,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

3
reference/translate.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9120</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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">
@ -21,6 +21,7 @@
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>

2
search.json
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1
sitemap.xml
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@ -3,6 +3,7 @@
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<url><loc>https://msberends.github.io/AMR/articles/MDR.html</loc></url>
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