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@ -31,7 +31,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -91,7 +91,7 @@
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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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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 30 April 2025.</p>
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generated on 01 May 2025.</p>
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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>
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@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2025-04-30</td>
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<td align="center">2025-05-01</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">S</td>
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<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2025-04-30</td>
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<td align="center">2025-05-01</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">S</td>
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<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2025-04-30</td>
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<td align="center">2025-05-01</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">R</td>
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@ -30,7 +30,7 @@
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -261,7 +261,7 @@ Length: 500<br>
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Levels: 5: S < SDD < I < R < NI<br>
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Available: 481 (96.2%, NA: 19 = 3.8%)<br>
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Unique: 3</p>
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<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>
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<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02/QJ01CR02)<br>
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Drug group: Beta-lactams/penicillins<br>
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%SI: 78.59%</p>
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<table class="table">
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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -30,7 +30,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -80,7 +80,7 @@
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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>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">30 April 2025</h4>
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<h4 data-toc-skip class="date">01 May 2025</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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<div class="d-none name"><code>datasets.Rmd</code></div>
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@ -424,19 +424,19 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
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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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you load the <code>AMR</code> package.</p>
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<p>It was last updated on 26 April 2025 14:23:14 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
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<p>It was last updated on 1 May 2025 09:48:49 UTC. Find more info about
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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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<p><strong>Direct download links:</strong></p>
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<ul>
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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> (43 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>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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</li>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx" class="external-link">Microsoft
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Excel workbook</a> (75 kB)<br>
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Excel workbook</a> (77 kB)<br>
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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.feather" class="external-link">Apache
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Feather file</a> (0.1 MB)<br>
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@ -445,7 +445,7 @@ Feather file</a> (0.1 MB)<br>
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Parquet file</a> (0.1 MB)<br>
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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
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SPSS Statistics data file</a> (0.3 MB)<br>
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SPSS Statistics data file</a> (0.4 MB)<br>
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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.dta" class="external-link">Stata
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DTA file</a> (10 kB)</li>
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@ -454,15 +454,15 @@ DTA file</a> (10 kB)</li>
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contain the ATC codes, common abbreviations, trade names and LOINC codes
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as comma separated values.</p>
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<p><strong>Example content</strong></p>
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<table class="table">
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<table style="width:100%;" class="table">
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<colgroup>
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<col width="1%">
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<col width="2%">
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<col width="8%">
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<col width="7%">
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<col width="7%">
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<col width="9%">
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<col width="12%">
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<col width="17%">
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<col width="16%">
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<col width="6%">
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<col width="16%">
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<col width="2%">
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@ -493,7 +493,7 @@ as comma separated values.</p>
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<td align="center">37768</td>
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<td align="center">Amikacin</td>
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<td align="center">Aminoglycosides</td>
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<td align="center">D06AX12, J01GB06, S01AA21</td>
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<td align="center">D06AX12, J01GB06, QD06AX12, …</td>
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<td align="center">Aminoglycoside antibacterials</td>
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<td align="center">Other aminoglycosides</td>
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<td align="center">ak, ami, amik, …</td>
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@ -509,7 +509,7 @@ as comma separated values.</p>
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<td align="center">33613</td>
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<td align="center">Amoxicillin</td>
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<td align="center">Beta-lactams/penicillins</td>
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<td align="center">J01CA04</td>
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<td align="center">J01CA04, QG51AA03, QJ01CA04</td>
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<td align="center">Beta-lactam antibacterials, penicillins</td>
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<td align="center">Penicillins with extended spectrum</td>
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<td align="center">ac, amox, amx</td>
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@ -525,7 +525,7 @@ as comma separated values.</p>
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<td align="center">23665637</td>
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<td align="center">Amoxicillin/clavulanic acid</td>
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<td align="center">Beta-lactams/penicillins</td>
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<td align="center">J01CR02</td>
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<td align="center">J01CR02, QJ01CR02</td>
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<td align="center">Beta-lactam antibacterials, penicillins</td>
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<td align="center">Combinations of penicillins, incl. beta-lactamase
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inhibitors</td>
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@ -542,7 +542,7 @@ inhibitors</td>
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<td align="center">6249</td>
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<td align="center">Ampicillin</td>
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<td align="center">Beta-lactams/penicillins</td>
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<td align="center">J01CA01, S01AA19</td>
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<td align="center">J01CA01, QJ01CA01, QJ51CA01, …</td>
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<td align="center">Beta-lactam antibacterials, penicillins</td>
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<td align="center">Penicillins with extended spectrum</td>
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<td align="center">am, amp, ampi</td>
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@ -558,7 +558,7 @@ inhibitors</td>
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<td align="center">447043</td>
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<td align="center">Azithromycin</td>
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<td align="center">Macrolides/lincosamides</td>
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<td align="center">J01FA10, S01AA26</td>
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<td align="center">J01FA10, QJ01FA10, QS01AA26, …</td>
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<td align="center">Macrolides, lincosamides and streptogramins</td>
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<td align="center">Macrolides</td>
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<td align="center">az, azi, azit, …</td>
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@ -574,7 +574,7 @@ inhibitors</td>
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<td align="center">5904</td>
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<td align="center">Benzylpenicillin</td>
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<td align="center">Beta-lactams/penicillins</td>
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<td align="center">J01CE01, S01AA14</td>
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<td align="center">J01CE01, QJ01CE01, QJ51CE01, …</td>
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<td align="center">Combinations of antibacterials</td>
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<td align="center">Combinations of antibacterials</td>
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<td align="center">bepe, pen, peni, …</td>
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -174,10 +174,7 @@ this shows on top of every sidebar to the right
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}
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}
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@media (max-width: 575.98px) {
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footer .pkgdown-footer-left {
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text-align: center;
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}
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footer .pkgdown-footer-right {
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footer * {
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text-align: center;
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}
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}
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27
index.html
27
index.html
@ -33,7 +33,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -145,9 +145,10 @@
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<span><span class="co">#> ℹ Using column 'mo' as input for mo_fullname()</span></span>
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<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_gram_negative()</span></span>
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<span><span class="co">#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
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<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per</span></span>
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<span><span class="co">#> session.</span></span>
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<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
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<span><span class="co">#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
|
||||
<span><span class="co">#> Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
|
||||
<span><span class="co">#> # A tibble: 35 × 7</span></span>
|
||||
<span><span class="co">#> bacteria GEN TOB AMK KAN IPM MEM </span></span>
|
||||
@ -173,9 +174,9 @@
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
|
||||
<span><span class="co">#> ℹ 502 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="14%">
|
||||
@ -292,8 +293,7 @@
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ 3 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="25%">
|
||||
@ -328,8 +328,7 @@
|
||||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
|
||||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
||||
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
|
||||
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span>
|
||||
<span><span class="co">#> ℹ 3 combinations had less than minimum = 30 results and were ignored</span></span></code></pre></div>
|
||||
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="19%">
|
||||
@ -422,13 +421,15 @@
|
||||
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
|
||||
<span><span class="co">#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
|
||||
<span><span class="co">#> ℹ For polymyxins() using column 'COL' (colistin)</span></span>
|
||||
<span><span class="co">#> Warning: There was 1 warning in `summarise()`.</span></span>
|
||||
<span><span class="co">#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
|
||||
<span><span class="co">#> ℹ In group 3: `ward = "Outpatient"`.</span></span>
|
||||
<span><span class="co">#> Caused by warning:</span></span>
|
||||
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).</span></span>
|
||||
<span><span class="co">#> ! Introducing NA: only 23 results available for KAN in group: ward =</span></span>
|
||||
<span><span class="co">#> "Outpatient" (minimum = 30).</span></span>
|
||||
<span><span class="va">out</span></span>
|
||||
<span><span class="co">#> # A tibble: 3 × 6</span></span>
|
||||
<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -49,11 +49,11 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9266" id="amr-2119266">AMR 2.1.1.9266<a class="anchor" aria-label="anchor" href="#amr-2119266"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9267" id="amr-2119267">AMR 2.1.1.9267<a class="anchor" aria-label="anchor" href="#amr-2119267"></a></h2>
|
||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
|
||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="tldr-2-1-1-9266">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9266"></a></h3>
|
||||
<h3 id="tldr-2-1-1-9267">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9267"></a></h3>
|
||||
<ul><li>
|
||||
<strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
|
||||
<li>
|
||||
@ -113,22 +113,22 @@
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="full-changelog-2-1-1-9266">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9266"></a></h3>
|
||||
<h3 id="full-changelog-2-1-1-9267">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9267"></a></h3>
|
||||
<div class="section level4">
|
||||
<h4 id="breaking-2-1-1-9266">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9266"></a></h4>
|
||||
<h4 id="breaking-2-1-1-9267">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9267"></a></h4>
|
||||
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
|
||||
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
|
||||
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
|
||||
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="new-2-1-1-9266">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9266"></a></h4>
|
||||
<h4 id="new-2-1-1-9267">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9267"></a></h4>
|
||||
<ul><li>
|
||||
<strong>One Health implementation</strong>
|
||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://amr-for-r.org/articles/datasets.html">download page</a>.</li>
|
||||
<li>The (new) <code>antimicrobials</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
|
||||
<li>The (new) <code>antimicrobials</code> data set contains all veterinary antimicrobials, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
|
||||
<li>
|
||||
<code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”)</li>
|
||||
<code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antimicrobials (that all start with “Q”)</li>
|
||||
<li>
|
||||
<code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</li>
|
||||
</ul></li>
|
||||
@ -176,7 +176,7 @@
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-2-1-1-9266">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9266"></a></h4>
|
||||
<h4 id="changed-2-1-1-9267">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9267"></a></h4>
|
||||
<ul><li>SIR interpretation
|
||||
<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
|
||||
<li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||
@ -232,15 +232,15 @@
|
||||
<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><a href="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
|
||||
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
|
||||
<li>
|
||||
<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
|
||||
<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule</li>
|
||||
<li>
|
||||
<code><a href="../reference/mo_property.html">mo_info()</a></code> now contains an extra element <code>rank</code> and <code>group_members</code> (with the contents of the new <code><a href="../reference/mo_property.html">mo_group_members()</a></code> function)</li>
|
||||
<li>Updated all ATC codes from WHOCC</li>
|
||||
<li>Updated all antibiotic DDDs from WHOCC</li>
|
||||
<li>Updated all antimicrobial DDDs from WHOCC</li>
|
||||
<li>Fix for using a manual value for <code>mo_transform</code> in <code><a href="../reference/antibiogram.html">antibiogram()</a></code>
|
||||
</li>
|
||||
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
|
||||
<li>Fix for mapping ‘high level’ antibiotics in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
|
||||
<li>Fix for mapping ‘high level’ antimicrobials in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
|
||||
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy, including the new function <code>as_reset_session()</code> to remove earlier coercions.</li>
|
||||
<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy, specifically:
|
||||
<ul><li>More weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species</li>
|
||||
@ -258,8 +258,8 @@
|
||||
<li>Added console colours support of <code>sir</code> class for Positron</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="other-2-1-1-9266">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9266"></a></h4>
|
||||
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="https://msberends.github.io/AMR/" class="external-link uri">https://msberends.github.io/AMR/</a>) will remain to work.</li>
|
||||
<h4 id="other-2-1-1-9267">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9267"></a></h4>
|
||||
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org/" class="external-link uri">http://amr-for-r.org/</a>) will remain to work.</li>
|
||||
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
|
||||
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
|
||||
<li>Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</li>
|
||||
@ -269,7 +269,7 @@
|
||||
</ul></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="older-versions-2-1-1-9266">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9266"></a></h3>
|
||||
<h3 id="older-versions-2-1-1-9267">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9267"></a></h3>
|
||||
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
|
||||
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
||||
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
||||
|
||||
@ -11,7 +11,7 @@ articles:
|
||||
PCA: PCA.html
|
||||
WHONET: WHONET.html
|
||||
WISCA: WISCA.html
|
||||
last_built: 2025-04-30T15:37Z
|
||||
last_built: 2025-05-01T09:52Z
|
||||
urls:
|
||||
reference: https://amr-for-r.org/reference
|
||||
article: https://amr-for-r.org/articles
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -172,7 +172,7 @@
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04" "QG51AA03" "QJ01CA04"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
|
||||
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
|
||||
@ -265,7 +265,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $atc</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04" "QG51AA03" "QJ01CA04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $atc_group1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
|
||||
@ -326,7 +326,7 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "S01AA19"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "QJ01CA01" "QJ51CA01" "QS01AA19" "S01AA19" </span>
|
||||
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span></span></span>
|
||||
@ -343,13 +343,13 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># use set_ab_names() for renaming columns</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
@ -418,6 +418,7 @@
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">set_ab_names()</span>: no atc found for column(s): "SXT" and "IPM"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -112,16 +112,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.83288 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.24932 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.40000 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.16438 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.49315 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.20548 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.19178 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.30137 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.67397 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.25753 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.83562 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.25205 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.40274 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.16712 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.49589 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.20822 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.19452 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.30411 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.67671 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.26027 21</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -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>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -87,7 +87,7 @@
|
||||
|
||||
<ul><li><p><code>av</code><br> Antiviral ID as used in this package (such as <code>ACI</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em> Combinations are codes that contain a <code>+</code> to indicate this, such as <code>ATA+COBI</code> for atazanavir/cobicistat.</p></li>
|
||||
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
|
||||
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, see <em>Details</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>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
|
||||
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
@ -109,8 +109,10 @@
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
|
||||
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and consequently only available where a CID is available.</p>
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>. Do note that ATC codes are not unique. For example, J01CR02 is officially the ATC code for "amoxicillin and beta-lactamase inhibitor". Consequently, these two items from the antimicrobials data set both return <code>"J01CR02"</code>:</p>
|
||||
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amoxicillin/clavulanic acid"</span><span class="op">)</span></span>
|
||||
<span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amoxicillin/sulbactam"</span><span class="op">)</span></span></code></pre><p></p></div>
|
||||
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and are consequently only available where a CID is available.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -164,13 +164,13 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span> <span class="co"># small spelling error</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span> <span class="co"># or a bit more severe</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span> <span class="co"># and even this works</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># use ab_* functions to get a specific properties (see ?ab_property);</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># they use as.ab() internally:</span></span></span>
|
||||
@ -185,6 +185,7 @@
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">set_ab_names()</span>: no atc found for column(s): "SXT" and "IPM"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></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;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||
@ -202,7 +203,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 37 more variables: J01CA04 <sir>, J01CR02 <sir>, J01CA01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01CR05 <sir>, J01DB04 <sir>, J01DE01 <sir>, J01DC02 <sir>, J01DC01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01DD01 <sir>, J01DD02 <sir>, J01DD04 <sir>, J01GB03 <sir>, J01GB01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, J01EE01 <sir>, J01XE01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, SXT <sir>, J01XE01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XX01 <sir>, J01XX08 <sir>, J01MA02 <sir>, J01MA14 <sir>, J01XA01 <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XA02 <sir>, J01AA07 <sir>, J01AA12 <sir>, J01AA02 <sir>, …</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -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>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -180,7 +180,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
|
||||
<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s to <code>"R"</code> only if the R breakpoint is missing. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s in these cases to <code>"R"</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
|
||||
@ -212,7 +212,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
|
||||
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the most efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
|
||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
|
||||
@ -353,7 +353,8 @@ 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;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
|
||||
@ -375,94 +376,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX CTX CAZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># example data sets, with combined MIC values and disk zones</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># create some example data sets, with combined MIC values and disk zones</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df_wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> amoxicillin <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
|
||||
@ -478,6 +393,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span> disks <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"EUCAST 2021"</span>, <span class="st">"EUCAST 2022"</span>, <span class="st">"EUCAST 2023"</span>, <span class="st">"EUCAST 2024"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># and clean previous SIR interpretation logs</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># most basic application:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||||
@ -486,23 +406,13 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14 × 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> <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> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pn… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escheric… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escheric… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escheric… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC amoxicillin Escheric… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC cipro Escheric… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK tobra Escheric… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK genta Escheric… human 18 </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> <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> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">09:53:45</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> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">09:53:45</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;"># 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>
|
||||
@ -675,34 +585,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 114 × 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> <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> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pneu human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_P… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_P… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 104 more rows</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;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># using parallel computing, which is available in base R</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># for single values</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||||
@ -741,6 +623,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 3 4 5 NA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 2 3 NA NA</span>
|
||||
@ -757,7 +640,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is_sir_eligible</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be the more impractical:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># example_isolates %>%</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># mutate(across(where(is_sir_eligible), as.sir))</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -135,6 +135,12 @@
|
||||
<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Loading required namespace: rvest</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QG51AA03. Please</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> check</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QJ01CA04. Please</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> check</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no.</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
@ -174,7 +174,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 37 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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 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> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
|
||||
@ -187,7 +187,7 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Fluc… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 29 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 27 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5 more variables: `P. mirabilis` <chr>, `S. aureus` <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `S. epidermidis` <chr>, `S. hominis` <chr>, `S. pneumoniae` <chr></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
|
||||
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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||||
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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||||
@ -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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -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="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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||||
@ -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="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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||||
@ -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="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
||||
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||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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|
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@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9266</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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Block a user