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30
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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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">
@ -87,7 +87,7 @@
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 02 October 2024.</p>
generated on 06 October 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-10-02</td>
<td align="center">2024-10-06</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">2024-10-02</td>
<td align="center">2024-10-06</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">2024-10-02</td>
<td align="center">2024-10-06</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -272,10 +272,11 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
<span><span class="co">#&gt; Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
<span><span class="co">#&gt; (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
<span><span class="co">#&gt; (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
<span><span class="co">#&gt; Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii</span></span>
<span><span class="co">#&gt; (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),</span></span>
<span><span class="co">#&gt; Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae</span></span>
<span><span class="co">#&gt; (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae</span></span>
<span><span class="co">#&gt; dissolvens (0.565)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
<span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
@ -295,11 +296,12 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus</span></span>
<span><span class="co">#&gt; phocae salmonis (0.552), Streptococcus pseudoporcinus (0.536),</span></span>
<span><span class="co">#&gt; Staphylococcus piscifermentans (0.533), Staphylococcus pseudintermedius</span></span>
<span><span class="co">#&gt; (0.532), Streptococcus gallolyticus pasteurianus (0.526), Salmonella</span></span>
<span><span class="co">#&gt; Portanigra (0.524), Streptococcus periodonticum (0.519), Streptococcus</span></span>
<span><span class="co">#&gt; phocae phocae (0.519), and Streptococcus pluranimalium (0.519)</span></span>
<span><span class="co">#&gt; phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),</span></span>
<span><span class="co">#&gt; Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans</span></span>
<span><span class="co">#&gt; (0.533), Staphylococcus pseudintermedius (0.532), Serratia</span></span>
<span><span class="co">#&gt; proteamaculans proteamaculans (0.526), Streptococcus gallolyticus</span></span>
<span><span class="co">#&gt; pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus</span></span>
<span><span class="co">#&gt; periodonticum (0.519)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Only the first 10 other matches of each record are shown. Run</span></span>
<span><span class="co">#&gt; print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>

3
articles/AMR_for_Python.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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">
@ -98,7 +98,6 @@ data in your own Python environment. This post will guide you through
setting up <code>rpy2</code> and show you how to use R functions from
<code>AMR</code> in Python to supercharge your antimicrobial resistance
analysis.</p>
<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="../AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
</div>
<div class="section level2">
<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>

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articles/EUCAST.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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2
articles/MDR.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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2
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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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2
articles/WHONET.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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6
articles/datasets.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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">
@ -76,7 +76,7 @@
<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">02 October 2024</h4>
<h4 data-toc-skip class="date">06 October 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>
@ -108,7 +108,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 2 October 2024 08:20:05 UTC. Find more info
<p>It was last updated on 4 October 2024 13:28:44 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>

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articles/index.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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2
articles/other_pkg.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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2
articles/resistance_predict.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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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