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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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website update since they are based on randomly created values and the
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 08 March 2026.</p>
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generated on 09 March 2026.</p>
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<div class="section level2">
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2026-03-08</td>
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<td align="center">2026-03-09</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2026-03-08</td>
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<td align="center">2026-03-09</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2026-03-08</td>
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<td align="center">2026-03-09</td>
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<td align="center">efgh</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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**Note:** values on this page will change with every website update
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**Note:** values on this page will change with every website update
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since they are based on randomly created values and the page was written
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since they are based on randomly created values and the page was written
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in [R Markdown](https://rmarkdown.rstudio.com/). However, the
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in [R Markdown](https://rmarkdown.rstudio.com/). However, the
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methodology remains unchanged. This page was generated on 08 March 2026.
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methodology remains unchanged. This page was generated on 09 March 2026.
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## Introduction
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## Introduction
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| date | patient_id | mo | AMX | CIP |
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| date | patient_id | mo | AMX | CIP |
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|:----------:|:----------:|:----------------:|:---:|:---:|
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|:----------:|:----------:|:----------------:|:---:|:---:|
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| 2026-03-08 | abcd | Escherichia coli | S | S |
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| 2026-03-09 | abcd | Escherichia coli | S | S |
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| 2026-03-08 | abcd | Escherichia coli | S | R |
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| 2026-03-09 | abcd | Escherichia coli | S | R |
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| 2026-03-08 | efgh | Escherichia coli | R | S |
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| 2026-03-09 | efgh | Escherichia coli | R | S |
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### Needed R packages
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### Needed R packages
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<main id="main" class="col-md-9"><div class="page-header">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
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<h4 data-toc-skip class="date">08 March 2026</h4>
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<h4 data-toc-skip class="date">09 March 2026</h4>
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<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>
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<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>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
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<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
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<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
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<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
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</h2>
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</h2>
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<p>A data set with 504 rows and 14 columns, containing the following
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<p>A data set with 505 rows and 14 columns, containing the following
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column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
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column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
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<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
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<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
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<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
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<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
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<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
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<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
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<p>This data set is in R available as <code>antimicrobials</code>, after
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<p>This data set is in R available as <code>antimicrobials</code>, after
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you load the <code>AMR</code> package.</p>
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you load the <code>AMR</code> package.</p>
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<p>It was last updated on 6 March 2026 17:53:42 UTC. Find more info
|
<p>It was last updated on 9 March 2026 10:57:36 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
|
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
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||||||
here</a>.</p>
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
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<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
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||||||
R Data Structure (RDS) file</a> (46 kB)<br>
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R Data Structure (RDS) file</a> (44 kB)<br>
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</li>
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</li>
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||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated
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||||||
text file</a> (0.1 MB)<br>
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text file</a> (0.1 MB)<br>
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||||||
@@ -442,7 +442,7 @@ Excel workbook</a> (79 kB)<br>
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Feather file</a> (0.1 MB)<br>
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Feather file</a> (0.1 MB)<br>
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</li>
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</li>
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||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet" class="external-link">Apache
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet" class="external-link">Apache
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Parquet file</a> (0.1 MB)<br>
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Parquet file</a> (94 kB)<br>
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</li>
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</li>
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||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav" class="external-link">IBM
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav" class="external-link">IBM
|
||||||
SPSS Statistics data file</a> (0.4 MB)<br>
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SPSS Statistics data file</a> (0.4 MB)<br>
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@@ -91,7 +91,7 @@ First 6 rows when filtering on genus *Escherichia*:
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## `antimicrobials`: Antibiotic and Antifungal Drugs
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## `antimicrobials`: Antibiotic and Antifungal Drugs
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A data set with 504 rows and 14 columns, containing the following column
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A data set with 505 rows and 14 columns, containing the following column
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names:
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names:
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*ab*, *cid*, *name*, *group*, *atc*, *atc_group1*, *atc_group2*,
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*ab*, *cid*, *name*, *group*, *atc*, *atc_group1*, *atc_group2*,
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*abbreviations*, *synonyms*, *oral_ddd*, *oral_units*, *iv_ddd*,
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*abbreviations*, *synonyms*, *oral_ddd*, *oral_units*, *iv_ddd*,
|
||||||
@@ -100,7 +100,7 @@ names:
|
|||||||
This data set is in R available as `antimicrobials`, after you load the
|
This data set is in R available as `antimicrobials`, after you load the
|
||||||
`AMR` package.
|
`AMR` package.
|
||||||
|
|
||||||
It was last updated on 6 March 2026 17:53:42 UTC. Find more info about
|
It was last updated on 9 March 2026 10:57:36 UTC. Find more info about
|
||||||
the contents, (scientific) source, and structure of this [data set
|
the contents, (scientific) source, and structure of this [data set
|
||||||
here](https://amr-for-r.org/reference/antimicrobials.html).
|
here](https://amr-for-r.org/reference/antimicrobials.html).
|
||||||
|
|
||||||
@@ -108,7 +108,7 @@ here](https://amr-for-r.org/reference/antimicrobials.html).
|
|||||||
|
|
||||||
- Download as [original R Data Structure (RDS)
|
- Download as [original R Data Structure (RDS)
|
||||||
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds)
|
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds)
|
||||||
(46 kB)
|
(44 kB)
|
||||||
- Download as [tab-separated text
|
- Download as [tab-separated text
|
||||||
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt)
|
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt)
|
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(0.1 MB)
|
(0.1 MB)
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@@ -120,7 +120,7 @@ here](https://amr-for-r.org/reference/antimicrobials.html).
|
|||||||
(0.1 MB)
|
(0.1 MB)
|
||||||
- Download as [Apache Parquet
|
- Download as [Apache Parquet
|
||||||
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet)
|
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet)
|
||||||
(0.1 MB)
|
(94 kB)
|
||||||
- Download as [IBM SPSS Statistics data
|
- Download as [IBM SPSS Statistics data
|
||||||
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav)
|
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav)
|
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(0.4 MB)
|
(0.4 MB)
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@@ -7,7 +7,7 @@
|
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|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -33,7 +33,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
3
llms.txt
3
llms.txt
@@ -724,6 +724,7 @@ or determine multi-drug resistant microorganisms (MDRO,
|
|||||||
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
|
[`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
@@ -865,7 +866,7 @@ information about how to work with functions in this package.
|
|||||||
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
|
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||||
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
|
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||||
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
|
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
|
||||||
Data Sets with 624 Antimicrobial Drugs
|
Data Sets with 625 Antimicrobial Drugs
|
||||||
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
|
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
|
||||||
: Data Set with Clinical Breakpoints for SIR Interpretation
|
: Data Set with Clinical Breakpoints for SIR Interpretation
|
||||||
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)
|
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -49,9 +49,9 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 class="pkg-version" data-toc-text="3.0.1.9032" id="amr-3019032">AMR 3.0.1.9032<a class="anchor" aria-label="anchor" href="#amr-3019032"></a></h2>
|
<h2 class="pkg-version" data-toc-text="3.0.1.9033" id="amr-3019033">AMR 3.0.1.9033<a class="anchor" aria-label="anchor" href="#amr-3019033"></a></h2>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="new-3-0-1-9032">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9032"></a></h4>
|
<h4 id="new-3-0-1-9033">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9033"></a></h4>
|
||||||
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
|
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code><mic></code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code><sir></code> columns to numeric</li>
|
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code><mic></code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code><sir></code> columns to numeric</li>
|
||||||
@@ -68,7 +68,7 @@
|
|||||||
</ul></li>
|
</ul></li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
|
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
|
||||||
<li>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
|
<li>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">ionophores()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>Support for Wildtype (WT) / Non-wildtype (NWT) in <code><a href="../reference/as.sir.html">as.sir()</a></code>, all plotting functions, and all susceptibility/resistance functions.
|
<li>Support for Wildtype (WT) / Non-wildtype (NWT) in <code><a href="../reference/as.sir.html">as.sir()</a></code>, all plotting functions, and all susceptibility/resistance functions.
|
||||||
<ul><li>
|
<ul><li>
|
||||||
@@ -84,7 +84,7 @@
|
|||||||
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
|
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="fixes-3-0-1-9032">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9032"></a></h4>
|
<h4 id="fixes-3-0-1-9033">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9033"></a></h4>
|
||||||
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
|
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
|
||||||
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
|
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
|
||||||
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
|
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
|
||||||
@@ -97,18 +97,18 @@
|
|||||||
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("<= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
|
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("<= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="updates-3-0-1-9032">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9032"></a></h4>
|
<h4 id="updates-3-0-1-9033">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9033"></a></h4>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>
|
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
|
<code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
|
||||||
|
<li>Added to the <code>antimicrobials</code> data set: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), and zorbamycin (<code>ZOR</code>)</li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.mic.html">rescale_mic()</a></code> gained the argument <code>round_to_next_log2</code>, which can be set to <code>TRUE</code> to round all values up to the nearest next log2 level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
|
<code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.mic.html">rescale_mic()</a></code> gained the argument <code>round_to_next_log2</code>, which can be set to <code>TRUE</code> to round all values up to the nearest next log2 level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
|
||||||
<li>
|
<li>
|
||||||
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
|
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
|
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
|
||||||
<li>Added to the <code>antimicrobials</code> data set: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), and zorbamycin (<code>ZOR</code>)</li>
|
|
||||||
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
|
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
|
||||||
<li>Updated handling of capped MIC values (<code><</code>, <code><=</code>, <code>></code>, <code>>=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
|
<li>Updated handling of capped MIC values (<code><</code>, <code><=</code>, <code>></code>, <code>>=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
|
||||||
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
|
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
|
||||||
|
|||||||
@@ -1,6 +1,6 @@
|
|||||||
# Changelog
|
# Changelog
|
||||||
|
|
||||||
## AMR 3.0.1.9032
|
## AMR 3.0.1.9033
|
||||||
|
|
||||||
#### New
|
#### New
|
||||||
|
|
||||||
@@ -19,6 +19,7 @@
|
|||||||
[`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
|
[`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
|
||||||
- Data set `esbl_isolates` to practise with AMR modelling
|
- Data set `esbl_isolates` to practise with AMR modelling
|
||||||
- AMR selectors
|
- AMR selectors
|
||||||
|
[`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||||
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||||
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
and
|
and
|
||||||
@@ -91,6 +92,10 @@
|
|||||||
and [`resistance()`](https://amr-for-r.org/reference/proportion.md)
|
and [`resistance()`](https://amr-for-r.org/reference/proportion.md)
|
||||||
gained the argument `guideline`, which defaults to EUCAST, for
|
gained the argument `guideline`, which defaults to EUCAST, for
|
||||||
interpreting the ‘I’ category correctly.
|
interpreting the ‘I’ category correctly.
|
||||||
|
- Added to the `antimicrobials` data set: cefepime/taniborbactam
|
||||||
|
(`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`),
|
||||||
|
kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`),
|
||||||
|
thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
|
||||||
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
|
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
|
||||||
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) gained
|
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) gained
|
||||||
the argument `round_to_next_log2`, which can be set to `TRUE` to round
|
the argument `round_to_next_log2`, which can be set to `TRUE` to round
|
||||||
@@ -102,10 +107,6 @@
|
|||||||
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
|
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
|
||||||
an argument `all_groups` to return all groups the antimicrobial drug
|
an argument `all_groups` to return all groups the antimicrobial drug
|
||||||
is in ([\#246](https://github.com/msberends/AMR/issues/246))
|
is in ([\#246](https://github.com/msberends/AMR/issues/246))
|
||||||
- Added to the `antimicrobials` data set: cefepime/taniborbactam
|
|
||||||
(`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`),
|
|
||||||
ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`),
|
|
||||||
xeruborbactam (`XER`), and zorbamycin (`ZOR`)
|
|
||||||
- Added explaining message to
|
- Added explaining message to
|
||||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
|
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
|
||||||
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
|
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
|
||||||
|
|||||||
@@ -10,7 +10,7 @@ articles:
|
|||||||
PCA: PCA.html
|
PCA: PCA.html
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
WISCA: WISCA.html
|
WISCA: WISCA.html
|
||||||
last_built: 2026-03-08T19:42Z
|
last_built: 2026-03-09T11:04Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://amr-for-r.org/reference
|
reference: https://amr-for-r.org/reference
|
||||||
article: https://amr-for-r.org/articles
|
article: https://amr-for-r.org/articles
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -112,16 +112,16 @@
|
|||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 26 26.68767 0</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 26 26.69041 0</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 58 58.10411 31</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 58 58.10685 31</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 60 60.25479 34</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 60 60.25753 34</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 46 46.01918 19</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 46 46.02192 19</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 76 76.34795 50</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 76 76.35068 50</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 79 79.06027 52</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 79 79.06301 52</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 86 86.04658 59</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 86 86.04932 59</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 38 38.15616 11</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 38 38.15890 11</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 28 28.52877 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 28 28.53151 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 48 48.11233 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 48 48.11507 21</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||||
|
|||||||
@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
|
|||||||
|
|
||||||
df
|
df
|
||||||
#> birth_date age age_exact age_at_y2k
|
#> birth_date age age_exact age_at_y2k
|
||||||
#> 1 1999-06-30 26 26.68767 0
|
#> 1 1999-06-30 26 26.69041 0
|
||||||
#> 2 1968-01-29 58 58.10411 31
|
#> 2 1968-01-29 58 58.10685 31
|
||||||
#> 3 1965-12-05 60 60.25479 34
|
#> 3 1965-12-05 60 60.25753 34
|
||||||
#> 4 1980-03-01 46 46.01918 19
|
#> 4 1980-03-01 46 46.02192 19
|
||||||
#> 5 1949-11-01 76 76.34795 50
|
#> 5 1949-11-01 76 76.35068 50
|
||||||
#> 6 1947-02-14 79 79.06027 52
|
#> 6 1947-02-14 79 79.06301 52
|
||||||
#> 7 1940-02-19 86 86.04658 59
|
#> 7 1940-02-19 86 86.04932 59
|
||||||
#> 8 1988-01-10 38 38.15616 11
|
#> 8 1988-01-10 38 38.15890 11
|
||||||
#> 9 1997-08-27 28 28.52877 2
|
#> 9 1997-08-27 28 28.53151 2
|
||||||
#> 10 1978-01-26 48 48.11233 21
|
#> 10 1978-01-26 48 48.11507 21
|
||||||
```
|
```
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<span></span>
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<span><span class="fu">glycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">glycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">ionophores</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||||
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<span></span>
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<span><span class="fu">isoxazolylpenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
|
<span><span class="fu">isoxazolylpenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
|
||||||
<span> return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
<span> return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
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@@ -234,6 +236,7 @@ my_data_with_all_these_columns %&gt;%
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<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
|
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
|
||||||
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
|
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
|
||||||
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)</p></li>
|
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)</p></li>
|
||||||
|
<li><p><code>ionophores()</code> can select: <br> lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)</p></li>
|
||||||
<li><p><code>isoxazolylpenicillins()</code> can select: <br> cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)</p></li>
|
<li><p><code>isoxazolylpenicillins()</code> can select: <br> cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)</p></li>
|
||||||
<li><p><code>lincosamides()</code> can select: <br> clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)</p></li>
|
<li><p><code>lincosamides()</code> can select: <br> clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)</p></li>
|
||||||
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>
|
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>
|
||||||
|
|||||||
@@ -55,6 +55,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
|
|||||||
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||||||
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
|
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
|
||||||
|
|
||||||
|
ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
|
||||||
|
|
||||||
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
|
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
|
||||||
return_all = TRUE, ...)
|
return_all = TRUE, ...)
|
||||||
|
|
||||||
@@ -459,6 +461,10 @@ quite slow in terms of performance.
|
|||||||
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN),
|
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN),
|
||||||
vancomycin-macromethod (VAM), and zorbamycin (ZOR)
|
vancomycin-macromethod (VAM), and zorbamycin (ZOR)
|
||||||
|
|
||||||
|
- `ionophores()` can select:
|
||||||
|
lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS),
|
||||||
|
and salinomycin (SAL)
|
||||||
|
|
||||||
- `isoxazolylpenicillins()` can select:
|
- `isoxazolylpenicillins()` can select:
|
||||||
cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC),
|
cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC),
|
||||||
meticillin (MET), oxacillin (OXA), and oxacillin screening test
|
meticillin (MET), oxacillin (OXA), and oxacillin screening test
|
||||||
|
|||||||
@@ -1,5 +1,5 @@
|
|||||||
<!DOCTYPE html>
|
<!DOCTYPE html>
|
||||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Sets with 624 Antimicrobial Drugs — antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Sets with 624 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
|
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Sets with 625 Antimicrobial Drugs — antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Sets with 625 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
|
||||||
The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
|
The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
|
||||||
The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||||
@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
|
||||||
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||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -46,7 +46,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
</nav><div class="container template-reference-topic">
|
</nav><div class="container template-reference-topic">
|
||||||
<div class="row">
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<div class="row">
|
||||||
<main id="main" class="col-md-9"><div class="page-header">
|
<main id="main" class="col-md-9"><div class="page-header">
|
||||||
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 624 Antimicrobial Drugs</h1>
|
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 625 Antimicrobial Drugs</h1>
|
||||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||||
<div class="d-none name"><code>antimicrobials.Rd</code></div>
|
<div class="d-none name"><code>antimicrobials.Rd</code></div>
|
||||||
</div>
|
</div>
|
||||||
@@ -69,7 +69,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||||
|
|
||||||
<div class="section">
|
<div class="section">
|
||||||
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 504 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
|
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 505 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
|
||||||
|
|
||||||
<ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
|
<ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||||
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
|
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||||
@@ -103,7 +103,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
|
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
|
|
||||||
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 504 rows and 14 columns.</p>
|
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 505 rows and 14 columns.</p>
|
||||||
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
|
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
@@ -145,9 +145,9 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 504 × 14</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 505 × 14</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
|
<span class="r-out co"><span class="r-pr">#></span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><named ></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><list></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Drugs for… Aminosali… <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Drugs for… Aminosali… <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
@@ -158,7 +158,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Beta-lact… Penicilli… <span style="color: #949494;"><chr [4]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Beta-lact… Penicilli… <span style="color: #949494;"><chr [4]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Beta-lact… Combinati… <span style="color: #949494;"><chr [6]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> Beta-lact… Combinati… <span style="color: #949494;"><chr [6]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… <span style="color: #949494;"><chr></span> <span style="color: #949494;"><chr></span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;"><chr [1]></span> <span style="color: #949494;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 494 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 495 more rows</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># iv_units <chr>, loinc <list></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># iv_units <chr>, loinc <list></span></span>
|
||||||
<span class="r-in"><span><span class="va">antivirals</span></span></span>
|
<span class="r-in"><span><span class="va">antivirals</span></span></span>
|
||||||
|
|||||||
@@ -1,4 +1,4 @@
|
|||||||
# Data Sets with 624 Antimicrobial Drugs
|
# Data Sets with 625 Antimicrobial Drugs
|
||||||
|
|
||||||
Two data sets containing all antimicrobials and antivirals. Use
|
Two data sets containing all antimicrobials and antivirals. Use
|
||||||
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) or one of the
|
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) or one of the
|
||||||
@@ -25,7 +25,7 @@ antivirals
|
|||||||
|
|
||||||
## Format
|
## Format
|
||||||
|
|
||||||
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 504 observations and 14 variables:
|
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 505 observations and 14 variables:
|
||||||
|
|
||||||
- `ab`
|
- `ab`
|
||||||
antimicrobial ID as used in this package (such as `AMC`), using the
|
antimicrobial ID as used in this package (such as `AMC`), using the
|
||||||
@@ -138,7 +138,7 @@ LOINC:
|
|||||||
[`av_property()`](https://amr-for-r.org/reference/av_property.md).
|
[`av_property()`](https://amr-for-r.org/reference/av_property.md).
|
||||||
|
|
||||||
An object of class `deprecated_amr_dataset` (inherits from `tbl_df`,
|
An object of class `deprecated_amr_dataset` (inherits from `tbl_df`,
|
||||||
`tbl`, `data.frame`) with 504 rows and 14 columns.
|
`tbl`, `data.frame`) with 505 rows and 14 columns.
|
||||||
|
|
||||||
An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with 120
|
An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with 120
|
||||||
rows and 11 columns.
|
rows and 11 columns.
|
||||||
@@ -219,9 +219,9 @@ unlike any other info from this package.** See
|
|||||||
|
|
||||||
``` r
|
``` r
|
||||||
antimicrobials
|
antimicrobials
|
||||||
#> # A tibble: 504 × 14
|
#> # A tibble: 505 × 14
|
||||||
#> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms
|
#> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms
|
||||||
#> <ab> <dbl> <chr> <lis> <lis> <chr> <chr> <list> <named >
|
#> <ab> <dbl> <chr> <lis> <lis> <chr> <chr> <list> <list>
|
||||||
#> 1 AMA 4649 4-ami… <chr> <chr> Drugs for… Aminosali… <chr [1]> <chr>
|
#> 1 AMA 4649 4-ami… <chr> <chr> Drugs for… Aminosali… <chr [1]> <chr>
|
||||||
#> 2 ACM 6450012 Acety… <chr> <chr> NA NA <chr [1]> <chr>
|
#> 2 ACM 6450012 Acety… <chr> <chr> NA NA <chr [1]> <chr>
|
||||||
#> 3 ASP 49787020 Acety… <chr> <chr> NA NA <chr [1]> <chr>
|
#> 3 ASP 49787020 Acety… <chr> <chr> NA NA <chr [1]> <chr>
|
||||||
@@ -232,7 +232,7 @@ antimicrobials
|
|||||||
#> 8 AMX 33613 Amoxi… <chr> <chr> Beta-lact… Penicilli… <chr [4]> <chr>
|
#> 8 AMX 33613 Amoxi… <chr> <chr> Beta-lact… Penicilli… <chr [4]> <chr>
|
||||||
#> 9 AMC 23665637 Amoxi… <chr> <chr> Beta-lact… Combinati… <chr [6]> <chr>
|
#> 9 AMC 23665637 Amoxi… <chr> <chr> Beta-lact… Combinati… <chr [6]> <chr>
|
||||||
#> 10 AXS 465441 Amoxi… <chr> <chr> NA NA <chr [1]> <chr>
|
#> 10 AXS 465441 Amoxi… <chr> <chr> NA NA <chr [1]> <chr>
|
||||||
#> # ℹ 494 more rows
|
#> # ℹ 495 more rows
|
||||||
#> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,
|
#> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,
|
||||||
#> # iv_units <chr>, loinc <list>
|
#> # iv_units <chr>, loinc <list>
|
||||||
antivirals
|
antivirals
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-08 <span style="color: #949494;">19:43:01</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-08 <span style="color: #949494;">19:43:01</span> 1 MIC cipro Escherich… human 0.256 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-08 <span style="color: #949494;">19:43:02</span> 1 DISK tobra Escherich… human 16 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 DISK tobra Escherich… human 16 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-08 <span style="color: #949494;">19:43:02</span> 1 DISK genta Escherich… human 18 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-09 <span style="color: #949494;">11:05:01</span> 1 DISK genta Escherich… human 18 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||||
|
|||||||
@@ -660,10 +660,10 @@ sir_interpretation_history()
|
|||||||
#> # A tibble: 4 × 18
|
#> # A tibble: 4 × 18
|
||||||
#> datetime index method ab_given mo_given host_given input_given
|
#> datetime index method ab_given mo_given host_given input_given
|
||||||
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
||||||
#> 1 2026-03-08 19:43:01 1 MIC amoxicillin Escherich… human 8
|
#> 1 2026-03-09 11:05:00 1 MIC amoxicillin Escherich… human 8
|
||||||
#> 2 2026-03-08 19:43:01 1 MIC cipro Escherich… human 0.256
|
#> 2 2026-03-09 11:05:00 1 MIC cipro Escherich… human 0.256
|
||||||
#> 3 2026-03-08 19:43:02 1 DISK tobra Escherich… human 16
|
#> 3 2026-03-09 11:05:00 1 DISK tobra Escherich… human 16
|
||||||
#> 4 2026-03-08 19:43:02 1 DISK genta Escherich… human 18
|
#> 4 2026-03-09 11:05:01 1 DISK genta Escherich… human 18
|
||||||
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
||||||
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
||||||
#> # breakpoint_S_R <chr>, site <chr>
|
#> # breakpoint_S_R <chr>, site <chr>
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -21,7 +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>
|
<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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -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>
|
<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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -147,7 +147,8 @@
|
|||||||
<span><span class="co">#></span></span>
|
<span><span class="co">#></span></span>
|
||||||
<span><span class="co">#> 1. If TZP is "R" then set to "R":</span></span>
|
<span><span class="co">#> 1. If TZP is "R" then set to "R":</span></span>
|
||||||
<span><span class="co">#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
|
<span><span class="co">#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
|
||||||
<p>These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
|
<p>These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminocoumarins<br>(clorobiocin, novobiocin, and penicillin/novobiocin)</p></li>
|
||||||
|
<li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
|
||||||
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
|
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
|
||||||
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
|
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
|
||||||
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
|
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
|
||||||
|
|||||||
@@ -135,9 +135,12 @@ TZP (piperacillin/tazobactam) is "R":
|
|||||||
#> 1. If TZP is "R" then set to "R":
|
#> 1. If TZP is "R" then set to "R":
|
||||||
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
|
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
|
||||||
|
|
||||||
These 42 antimicrobial groups are allowed in the rules
|
These 43 antimicrobial groups are allowed in the rules
|
||||||
(case-insensitive) and can be used in any combination:
|
(case-insensitive) and can be used in any combination:
|
||||||
|
|
||||||
|
- aminocoumarins
|
||||||
|
(clorobiocin, novobiocin, and penicillin/novobiocin)
|
||||||
|
|
||||||
- aminoglycosides
|
- aminoglycosides
|
||||||
(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
|
(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
|
||||||
bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
|
bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -144,7 +144,7 @@
|
|||||||
<span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins_2nd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #2"</span>,</span>
|
<span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins_2nd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #2"</span>,</span>
|
||||||
<span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #3"</span></span>
|
<span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #3"</span></span>
|
||||||
<span><span class="op">)</span></span></code></pre><p></p></div>
|
<span><span class="op">)</span></span></code></pre><p></p></div>
|
||||||
<p>All 42 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
|
<p>All 43 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, and ampicillin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, and ampicillin</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <br> amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <br> amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
|
||||||
@@ -159,6 +159,7 @@
|
|||||||
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> can select: <br> ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> can select: <br> ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> can select: <br> besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> can select: <br> besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin</p></li>
|
||||||
|
<li><p><code><a href="antimicrobial_selectors.html">ionophores()</a></code> can select: <br> lasalocid, monensin sodium, narasin, nystatin, and salinomycin</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> can select: <br> cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> can select: <br> cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin</p></li>
|
||||||
<li><p><code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> can select: <br> dalbavancin, oritavancin, and telavancin</p></li>
|
<li><p><code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> can select: <br> dalbavancin, oritavancin, and telavancin</p></li>
|
||||||
|
|||||||
@@ -126,7 +126,7 @@ antimicrobial group:
|
|||||||
all(glycopeptides() == "R") ~ "My MDRO #3"
|
all(glycopeptides() == "R") ~ "My MDRO #3"
|
||||||
)
|
)
|
||||||
|
|
||||||
All 42 antimicrobial selectors are supported for use in the rules:
|
All 43 antimicrobial selectors are supported for use in the rules:
|
||||||
|
|
||||||
- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
can select:
|
can select:
|
||||||
@@ -312,6 +312,10 @@ All 42 antimicrobial selectors are supported for use in the rules:
|
|||||||
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
|
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
|
||||||
vancomycin, vancomycin-macromethod, and zorbamycin
|
vancomycin, vancomycin-macromethod, and zorbamycin
|
||||||
|
|
||||||
|
- [`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
|
can select:
|
||||||
|
lasalocid, monensin sodium, narasin, nystatin, and salinomycin
|
||||||
|
|
||||||
- [`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
- [`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
can select:
|
can select:
|
||||||
cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and
|
cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and
|
||||||
|
|||||||
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|||||||
|
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||||||
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|
||||||
|
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
|
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|
||||||
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||||||
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||||||
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
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||||||
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||||||
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@@ -9,7 +9,7 @@
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|||||||
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
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||||||
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|||||||
@@ -7,7 +7,7 @@
|
|||||||
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
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@@ -7,7 +7,7 @@
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|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
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|
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|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
|
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||||||
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|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
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|
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|
||||||
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
|
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|
||||||
|
|
||||||
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|
||||||
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|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
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|
||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
||||||
@@ -263,7 +263,7 @@
|
|||||||
|
|
||||||
<dt>
|
<dt>
|
||||||
|
|
||||||
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">peptides()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
|
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">ionophores()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">peptides()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
|
||||||
|
|
||||||
</dt>
|
</dt>
|
||||||
<dd>Antimicrobial Selectors</dd>
|
<dd>Antimicrobial Selectors</dd>
|
||||||
@@ -393,7 +393,7 @@
|
|||||||
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
|
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
|
||||||
|
|
||||||
</dt>
|
</dt>
|
||||||
<dd>Data Sets with 624 Antimicrobial Drugs</dd>
|
<dd>Data Sets with 625 Antimicrobial Drugs</dd>
|
||||||
|
|
||||||
<dt>
|
<dt>
|
||||||
|
|
||||||
|
|||||||
@@ -252,6 +252,7 @@ or determine multi-drug resistant microorganisms (MDRO,
|
|||||||
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
|
[`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||||
@@ -393,7 +394,7 @@ information about how to work with functions in this package.
|
|||||||
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
|
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||||
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
|
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||||
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
|
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
|
||||||
Data Sets with 624 Antimicrobial Drugs
|
Data Sets with 625 Antimicrobial Drugs
|
||||||
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
|
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
|
||||||
: Data Set with Clinical Breakpoints for SIR Interpretation
|
: Data Set with Clinical Breakpoints for SIR Interpretation
|
||||||
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)
|
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)
|
||||||
|
|||||||
@@ -13,7 +13,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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||||||
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||||||
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|
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||||||
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8
reference/ionophores.html
Normal file
8
reference/ionophores.html
Normal file
@@ -0,0 +1,8 @@
|
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|
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|
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|
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||||||
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|
||||||
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||||||
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|
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||||||
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|
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|
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|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
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|
||||||
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|
||||||
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|
||||||
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|
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||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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||||||
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
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||||||
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||||||
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|
||||||
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@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
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|
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|
||||||
|
|
||||||
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
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|
||||||
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|
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||||||
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
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@@ -7,7 +7,7 @@
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
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|||||||
@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
|
|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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||||||
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||||||
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
|
||||||
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||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
|
||||||
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||||||
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|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">3.0.1.9032</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
|
||||||
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|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
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File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user