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@ -36,7 +36,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
<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="">2.1.1.9004</small>
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@ -204,7 +204,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 13 February 2024.</p>
generated on 24 February 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-02-13</td>
<td align="center">2024-02-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

2
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
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@ -401,19 +401,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S R S S S S</span></span>
<span><span class="co">#&gt; 2 R S S S I I</span></span>
<span><span class="co">#&gt; 3 I S I R R S</span></span>
<span><span class="co">#&gt; 4 R R S S S S</span></span>
<span><span class="co">#&gt; 5 R R S I R I</span></span>
<span><span class="co">#&gt; 6 I R I I I R</span></span>
<span><span class="co">#&gt; 1 S I R I S I</span></span>
<span><span class="co">#&gt; 2 S R I S S R</span></span>
<span><span class="co">#&gt; 3 S I S R I S</span></span>
<span><span class="co">#&gt; 4 I S R R S S</span></span>
<span><span class="co">#&gt; 5 S R R S S I</span></span>
<span><span class="co">#&gt; 6 R S S I R S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -454,40 +454,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4197</td>
<td align="right">83.94%</td>
<td align="right">946</td>
<td align="right">18.92%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">260</td>
<td align="right">5.20%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
<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="">2.1.1.9004</small>
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@ -193,7 +193,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">13 February 2024</h4>
<h4 data-toc-skip class="date">24 February 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -532,7 +532,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
<p>It was last updated on 24 February 2024 14:16:52 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -543,7 +543,7 @@ R Data Structure (RDS) file</a> (44 kB)<br>
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
Excel workbook</a> (72 kB)<br>
Excel workbook</a> (73 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br>
@ -904,40 +904,40 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 29 747 rows and 12 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>method</em>, <em>site</em>,
<em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>,
<em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em>, and
<em>uti</em>.</p>
<p>A data set with 29 883 rows and 13 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</em>,
<em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>,
<em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>,
<em>breakpoint_R</em>, and <em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 13:07:11 UTC. Find more info
<p>It was last updated on 24 February 2024 14:16:52 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (59 kB)<br>
R Data Structure (RDS) file</a> (61 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (2.3 MB)<br>
text file</a> (2.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.3 MB)<br>
Excel workbook</a> (1.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.2 MB)<br>
Feather file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (96 kB)<br>
Parquet file</a> (91 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (7.9 MB)<br>
transport (XPT) file</a> (8.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (4.6 MB)<br>
SPSS Statistics data file</a> (4.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (7.8 MB)</li>
DTA file</a> (8.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
@ -973,13 +973,14 @@ use.</p>
<colgroup>
<col width="6%">
<col width="3%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="7%">
<col width="14%">
<col width="6%">
<col width="2%">
<col width="16%">
<col width="15%">
<col width="8%">
<col width="8%">
<col width="7%">
@ -989,6 +990,7 @@ use.</p>
<thead><tr class="header">
<th align="center">guideline</th>
<th align="center">type</th>
<th align="center">host</th>
<th align="center">method</th>
<th align="center">site</th>
<th align="center">mo</th>
@ -1006,6 +1008,7 @@ use.</p>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
@ -1022,6 +1025,7 @@ use.</p>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
@ -1038,6 +1042,7 @@ use.</p>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
@ -1054,6 +1059,7 @@ use.</p>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
@ -1070,6 +1076,7 @@ use.</p>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
@ -1086,6 +1093,7 @@ use.</p>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>

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@ -10,7 +10,7 @@
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@ -38,7 +38,7 @@
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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@ -164,10 +164,6 @@
<p><strong>Matthijs S. Berends</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Christian F. Luz</strong>. Author, contributor. <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Dennis Souverein</strong>. Author, contributor. <a href="https://orcid.org/0000-0003-0455-0336" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
@ -208,6 +204,10 @@
<p><strong>Annick Lenglet</strong>. Contributor. <a href="https://orcid.org/0000-0003-2013-8405" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Christian F. Luz</strong>. Contributor. <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Bart C. Meijer</strong>. Contributor.
</p>
@ -228,10 +228,18 @@
<p><strong>Sofia Ny</strong>. Contributor. <a href="https://orcid.org/0000-0002-2017-1363" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Matthew Saab</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Jonas Salm</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Javier Sanchez</strong>. Contributor. <a href="https://orcid.org/0000-0003-2605-8094" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Rogier P. Schade</strong>. Contributor.
</p>
@ -240,6 +248,10 @@
<p><strong>Bhanu N. M. Sinha</strong>. Thesis advisor. <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Jason Stull</strong>. Contributor. <a href="https://orcid.org/0000-0002-9028-8153" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
<li>
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>

4
extra.js
View File

@ -58,8 +58,8 @@ $(document).ready(function() {
// contributors
x = x.replace("Alex", "Prof. Alex");
x = x.replace("Andrew", "Dr. Andrew");
x = x.replace("Anthony", "Dr. Anthony");
x = x.replace("Annick", "Dr. Annick");
x = x.replace("Anthony", "Dr. Anthony");
x = x.replace("Bart", "Dr. Bart");
x = x.replace("Bhanu", "Prof. Bhanu");
x = x.replace("Casper", "Prof. Casper");
@ -67,6 +67,8 @@ $(document).ready(function() {
x = x.replace("Corinna", "Dr. Corinna");
x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Gwen", "Dr. Gwen");
x = x.replace("Jason", "Dr. Jason");
x = x.replace("Javier", "Prof. Javier");
x = x.replace("Jonas", "Dr. Jonas");
x = x.replace("Judith", "Dr. Judith");
x = x.replace("Matthijs", "Dr. Matthijs");

5
index.html
View File

@ -42,7 +42,7 @@
<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="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -779,7 +779,7 @@
<p>Manually, using:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
@ -851,7 +851,6 @@
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>Matthijs S. Berends <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Christian F. Luz <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Dennis Souverein <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0003-0455-0336" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Erwin E. A. Hassing <br><small class="roles"> Author, contributor </small> </li>
<li><a href="authors.html">More about authors...</a></li>

30
news/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -159,21 +159,31 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9004" id="amr-2119004">AMR 2.1.1.9004<a class="anchor" aria-label="anchor" href="#amr-2119004"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9008" id="amr-2119008">AMR 2.1.1.9008<a class="anchor" aria-label="anchor" href="#amr-2119008"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)</em></p>
<div class="section level3">
<h3 id="breaking-2-1-1-9004">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9004"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents a year ago</li>
<h3 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9008">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9008"></a></h3>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change. * <code><a href="../reference/as.sir.html">as.sir()</a></code> now supports animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names. * The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>. * The <code>antibiotics</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * <code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”) * <code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9008">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9008"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9004">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9004"></a></h3>
<ul><li>Function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
<h3 id="new-functions-2-1-1-9008">New functions<a class="anchor" aria-label="anchor" href="#new-functions-2-1-1-9008"></a></h3>
<ul><li>The group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>
<code><a href="../reference/as.mic.html">limit_mic_range()</a></code>, which allows to limit MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
</ul><div class="section level4">
<h4 id="changed-2-1-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9004"></a></h4>
<h4 id="changed-2-1-1-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9008"></a></h4>
<ul><li>For MICs:
<ul><li>Added 4096 and 5 powers of 192 as valid levels (192, 384, 576, 768, 960)</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>.</li>
<ul><li>Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">limit_mic_range()</a></code> and <code>scale_*_mic()</code> functions.</li>
</ul></li>
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML</li>
<li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">dplyr::rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">dplyr::c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
<li>Updated all ATC codes from WHOCC</li>
<li>Updated all antibiotic DDDs from WHOCC</li>
</ul></div>
</div>
</div>

2
pkgdown.yml
View File

@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2024-02-13T12:50Z
last_built: 2024-02-24T17:55Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

22
reference/AMR-options.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -168,17 +168,17 @@
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
<ul><li><p><code>AMR_custom_ab</code> <br> Allows to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> Allows to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> Used for setting the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2023"</code>. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).</p></li>
<ul><li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2023"</code>. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
<li><p><code>AMR_ecoff</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is <code>FALSE</code>.</p></li>
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>
<li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>.</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_locale</code> <br> A language to use for the <code>AMR</code> package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported).</p></li>
<li><p><code>AMR_locale</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the language for the <code>AMR</code> package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).</p></li>
<li><p><code>AMR_mo_source</code> <br> A file location for a manual code list to be used in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions. This is explained in <code><a href="mo_source.html">set_mo_source()</a></code>.</p></li>
</ul></div>
<div class="section level2">
@ -187,14 +187,14 @@
<p>Settings in <span style="R">R</span> are not saved globally and are thus lost when <span style="R">R</span> is exited. You can save your options to your own <code>.Rprofile</code> file, which is a user-specific file. You can edit it using:</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>In this file, you can set options such as:</p>
<p>In this file, you can set options such as...</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_include_PKPD <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div>
<p>to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with <code><a href="as.sir.html">as.sir()</a></code>.</p><div class="section">
<p>...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with <code><a href="as.sir.html">as.sir()</a></code>.</p><div class="section">
<h3 id="share-options-within-team">Share Options Within Team<a class="anchor" aria-label="anchor" href="#share-options-within-team"></a></h3>
<p>For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:</p><ol><li><p>Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.</p></li>
<p>For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:</p><ol><li><p>Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.</p></li>
<li><p>For each user, open the <code>.Rprofile</code> file using <code>utils::file.edit("~/.Rprofile")</code> and put in there:</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="kw"><a href="https://rdrr.io/r/base/source.html" class="external-link">source</a></span><span class="op">(</span><span class="st">"X:/team_folder/R_options.R"</span><span class="op">)</span></span></code></pre><p></p></div></li>
<li><p>Reload R/RStudio and check the settings with <code><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption()</a></code>, e.g. <code>getOption("AMR_locale")</code> if you have set that value.</p></li>

15
reference/AMR.html
View File

@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated december 2022) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated January 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>
@ -220,8 +220,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p><strong>Maintainer</strong>: Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p>
<p>Authors:</p><ul><li><p>Christian F. Luz (<a href="https://orcid.org/0000-0001-5809-5995" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
<p>Authors:</p><ul><li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Erwin E. A. Hassing [contributor]</p></li>
</ul><p>Other contributors:</p><ul><li><p>Casper J. Albers (<a href="https://orcid.org/0000-0002-9213-6743" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Peter Dutey-Magni (<a href="https://orcid.org/0000-0002-8942-9836" class="external-link">ORCID</a>) [contributor]</p></li>
@ -231,14 +230,18 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<li><p>Eric H. L. C. M. Hazenberg [contributor]</p></li>
<li><p>Gwen Knight (<a href="https://orcid.org/0000-0002-7263-9896" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Annick Lenglet (<a href="https://orcid.org/0000-0003-2013-8405" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Christian F. Luz (<a href="https://orcid.org/0000-0001-5809-5995" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Bart C. Meijer [contributor]</p></li>
<li><p>Dmytro Mykhailenko [contributor]</p></li>
<li><p>Anton Mymrikov [contributor]</p></li>
<li><p>Andrew P. Norgan (<a href="https://orcid.org/0000-0002-2955-2066" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Sofia Ny (<a href="https://orcid.org/0000-0002-2017-1363" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Matthew Saab [contributor]</p></li>
<li><p>Jonas Salm [contributor]</p></li>
<li><p>Javier Sanchez (<a href="https://orcid.org/0000-0003-2605-8094" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Rogier P. Schade [contributor]</p></li>
<li><p>Bhanu N. M. Sinha (<a href="https://orcid.org/0000-0003-1634-0010" class="external-link">ORCID</a>) [thesis advisor]</p></li>
<li><p>Jason Stull (<a href="https://orcid.org/0000-0002-9028-8153" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Anthony Underwood (<a href="https://orcid.org/0000-0002-8547-4277" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Anita Williams (<a href="https://orcid.org/0000-0002-5295-8451" class="external-link">ORCID</a>) [contributor]</p></li>
</ul></div>

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@ -10,7 +10,7 @@
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@ -222,16 +222,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.19126 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 43 43.95355 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.28415 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 76 76.99727 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 83 83.98361 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.09290 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.46448 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.04918 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.65847 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.51093 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.22131 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 43 43.98361 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.31421 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.02732 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.01366 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.12295 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.49454 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.07923 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.68852 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.54098 13</span>
</code></pre></div>
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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<li><p><code>atc_group2</code><br> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</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>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 174 drugs</p></li>
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs</p></li>
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs</p></li>
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs</p></li>
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br> All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
</ul></div>

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@ -300,8 +300,8 @@
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on January 8th, 2024.</p></li>
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
@ -325,7 +325,7 @@
</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, or <em>Wuchereria</em>;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kodamaea</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Verticillium</em>, or <em>Wuchereria</em>;</p></li>
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>

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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "ECOFF", "animal", and "human".
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.'><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content='Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "ECOFF", "animal", and "human".
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.'><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently breakpoints are available:
For clinical microbiology from EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology from EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently breakpoints are available:
For clinical microbiology from EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology from EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -14,7 +24,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<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="">2.1.1.9004</small>
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@ -164,9 +174,11 @@ All breakpoints used for interpretation are publicly available in the clinical_b
</div>
<div class="ref-description section level2">
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
<p>Currently available <strong>breakpoint guidelines</strong> are EUCAST 2011-2023 and CLSI 2011-2023, and available <strong>breakpoint types</strong> are "ECOFF", "animal", and "human".</p>
<p>All breakpoints used for interpretation are publicly available in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
<p>Currently breakpoints are available:</p><ul><li><p>For <strong>clinical microbiology</strong> from EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
<li><p>For <strong>veterinary microbiology</strong> from EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
</ul><p>All breakpoints used for interpretation are publicly available in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
<div class="section level2">
@ -192,6 +204,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
<span> host <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -207,6 +220,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
<span> host <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -222,21 +236,19 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span></span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
<span> host <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An object of class <code>sir</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01//" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01//</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@ -289,7 +301,11 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dt>breakpoint_type</dt>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>.</p></dd>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
<dt>host</dt>
<dd><p>a vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
<dt>col_mo</dt>
@ -310,19 +326,25 @@ All breakpoints used for interpretation are publicly available in the clinical_b
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><em>Note: The clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a> and the public use of this <code>AMR</code> package has been endorsed by CLSI and EUCAST, please see <a href="clinical_breakpoints.html">clinical_breakpoints</a> for more information.</em></p><div class="section">
<p><em>Note: The clinical breakpoints in this package were validated through, and imported from, <a href="https://whonet.org" class="external-link">WHONET</a>. The public use of this <code>AMR</code> package has been endorsed by both CLSI and EUCAST. See <a href="clinical_breakpoints.html">clinical_breakpoints</a> for more information.</em></p><div class="section">
<h3 id="how-it-works">How it Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a></h3>
<p>The <code>as.sir()</code> function works in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.mic, as.sir)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.mic), as.sir))</span></code></pre><p></p></div></li>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.mic), as.sir))</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"># for veterinary breakpoints, also set `host`:</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.mic, as.sir, <span class="at">host =</span> <span class="st">"column_with_animal_hosts"</span>, <span class="at">guideline =</span> <span class="st">"CLSI"</span>)</span></code></pre><p></p></div></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.disk, as.sir)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.disk), as.sir))</span></code></pre><p></p></div></li>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.disk), as.sir))</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"># for veterinary breakpoints, also set `host`:</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.disk, as.sir, <span class="at">host =</span> <span class="st">"column_with_animal_hosts"</span>, <span class="at">guideline =</span> <span class="st">"CLSI"</span>)</span></code></pre><p></p></div></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.sir(your_data)</code>.</p></li>
</ol><p><strong>For points 2, 3 and 4: Use <code>sir_interpretation_history()</code></strong> to retrieve a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> (or <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> if the <code>tibble</code> package is installed) with all results of the last <code>as.sir()</code> call.</p>
@ -332,7 +354,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023).</p>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023.</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2023"</code> or <code>"CLSI 2023"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
@ -340,6 +362,9 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="co"># or to reset:</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="cn">NULL</span>)</span></code></pre><p></p></div>
<p>For veterinary guidelines, these might be the best options:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_breakpoint_type =</span> <span class="st">"animal"</span>)</span></code></pre><p></p></div>
</div>
<div class="section">
@ -353,7 +378,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 29 747 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 29 883 rows and 13 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">
@ -557,31 +582,31 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming an unspecified body site. Use argument uti to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo input</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-02-13 <span style="color: #949494;">12:51:29</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-02-13 <span style="color: #949494;">12:51:29</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-02-13 <span style="color: #949494;">12:51:29</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-02-13 <span style="color: #949494;">12:51:29</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-02-13 <span style="color: #949494;">12:51:24</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-02-13 <span style="color: #949494;">12:51:24</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-02-13 <span style="color: #949494;">12:51:24</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-02-13 <span style="color: #949494;">12:51:24</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-02-13 <span style="color: #949494;">12:51:24</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-02-13 <span style="color: #949494;">12:51:23</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-02-13 <span style="color: #949494;">12:51:23</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-02-13 <span style="color: #949494;">12:51:23</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-02-13 <span style="color: #949494;">12:51:23</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-02-24 <span style="color: #949494;">17:56:35</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-02-24 <span style="color: #949494;">17:56:35</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-02-24 <span style="color: #949494;">17:56:35</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-02-24 <span style="color: #949494;">17:56:34</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-02-24 <span style="color: #949494;">17:56:30</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-02-24 <span style="color: #949494;">17:56:29</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-02-24 <span style="color: #949494;">17:56:29</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-02-24 <span style="color: #949494;">17:56:29</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, host &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-in"><span></span></span>
<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>

2
reference/atc_online.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/av_from_text.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/av_property.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/availability.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/bug_drug_combinations.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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
reference/clinical_breakpoints.html
View File

@ -1,5 +1,11 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use as.sir() to transform MICs or disks measurements to SIR values."><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
Use as.sir() to transform MICs or disks measurements to SIR values."><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -160,7 +166,10 @@
</div>
<div class="ref-description section level2">
<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2023 and CLSI 2011-2023.</p>
<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2023 and CLSI 2019-2023.</p>
<p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
</div>
<div class="section level2">
@ -170,8 +179,9 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 29 747 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 29 883 observations and 13 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"</p></li>
<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
@ -225,21 +235,22 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 29,747 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline type method site mo rank_index ab ref_tbl disk_dose</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… 10ug </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… 1.25ug/2…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo… 30ug/6ug </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto… 30ug </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2… human DISK Unco… B_ACNTB 3 AMK Acineto… 30ug </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2… human MIC Unco… B_ACNTB 3 AMK Acineto… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 29,737 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 3 more variables: breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 29,883 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline type host method site mo rank_index ab ref_tbl </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 29,873 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># uti &lt;lgl&gt;</span></span>
</code></pre></div>
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@ -263,19 +263,19 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 41 39 26 40 18 36 15 39 18 45 32 27 10 2 13 24 43 12 8 5 3 12 31 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 16 4 1 26 32 27 21 45 42 17 16 21 8 4 30 1 17 25 34 5 10 1 18 44 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 4 46 6 12 43 2 43 45 37 33 18 38 45 36 46 4 35 40 12 7 11 23 10 35 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 4 5 29 27 41 12 30 45 18 47 22 28 39 19 27 45 16 4 21 40 39 39 10 6 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 29 45 31 14 41 39 26 40 18 36 15 39 18 45 32 27 10 2 13 24 43 12 8 5 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 12 31 9 16 4 1 26 32 27 21 45 42 17 16 21 8 4 30 1 17 25 34 5 10 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 18 44 33 4 6 12 43 2 43 45 37 33 18 38 45 36 46 4 35 40 12 7 11 23 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 35 20 4 5 29 27 41 12 30 45 18 46 22 28 39 19 27 45 16 4 21 40 39 39 10</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
@ -317,16 +317,16 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 036063 2010-01-28 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 077922 2009-08-18 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 036063 2010-01-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 077922 2009-08-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 080086 2010-08-08 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 0DBF93 2015-10-12 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 105248 2005-06-16 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 114570 2003-04-08 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 119392 2010-11-01 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 119392 2010-11-01 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 161740 2005-06-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 174209 2011-10-03 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 210105 2009-06-13 B TRUE </span>
@ -343,7 +343,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [96]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2010-01-28 036063 1 TRUE </span>
@ -371,8 +371,8 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 62 12 36 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 24 9 17 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 63 12 35 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 24 9 17 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 9 7 7 9</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -405,16 +405,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [96]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 5B78D5 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E52625 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 645121 B_SERRT_MRCS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 807228 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> D41749 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 210105 B_ENTRC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 789292 B_STRPT_SLVR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 551943 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D81C77 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A24795 B_BCTRD_FRGL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 686445 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D39422 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 298662 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 5B78D5 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E52625 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 645121 B_SERRT_MRCS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 807228 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D41749 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 210105 B_ENTRC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 789292 B_STRPT_SLVR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/ggplot_sir.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/guess_ab_col.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

6
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -170,7 +170,7 @@
<dl><dt>
<code><a href="AMR.html">AMR</a></code> <code><a href="AMR.html">AMR-package</a></code>
<code><a href="AMR.html">AMR-package</a></code> <code><a href="AMR.html">AMR</a></code>
</dt>
<dd>The <code>AMR</code> Package</dd>
</dl></div><div class="section level2">
@ -258,7 +258,7 @@
<dd>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data</dd>
</dl><dl><dt>
<code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">rescale_mic()</a></code> <code><a href="as.mic.html">droplevels(<i>&lt;mic&gt;</i>)</a></code>
<code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">limit_mic_range()</a></code> <code><a href="as.mic.html">droplevels(<i>&lt;mic&gt;</i>)</a></code>
</dt>
<dd>Transform Input to Minimum Inhibitory Concentrations (MIC)</dd>
</dl><dl><dt>

2
reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/italicise_taxonomy.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</small>
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2
reference/join.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

2
reference/key_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">

6
reference/kurtosis.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</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">
@ -199,9 +199,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.964789</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.021297</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04107091</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.08143396</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</small>
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4
reference/mdro.html
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8
reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</small>
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@ -218,10 +218,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S I I S I I R I I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R S I I S I I R I</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.449138 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 1.449138 -0.621059</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>

2
reference/microorganisms.codes.html
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</div>
<div class="ref-description section level2">
<p>A data set containing the full microbial taxonomy (<strong>last updated: December 11th, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
<p>A data set containing the full microbial taxonomy (<strong>last updated: January 8th, 2024</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div class="section level2">
@ -184,7 +184,7 @@
<li><p><code>gbif_parent</code><br> GBIF identifier of the parent taxon</p></li>
<li><p><code>gbif_renamed_to</code><br> GBIF identifier of the currently valid taxon</p></li>
<li><p><code>source</code><br> Either "GBIF", "LPSN", or "manually added" (see <em>Source</em>)</p></li>
<li><p><code>prevalence</code><br> Prevalence of the microorganism according to Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
<li><p><code>prevalence</code><br> Prevalence of the microorganism based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
), see <code><a href="mo_matching_score.html">mo_matching_score()</a></code> for the full explanation</p></li>
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
</ul></div>
@ -193,8 +193,8 @@
<ul><li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on January 8th, 2024.</p></li>
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>

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</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, or <em>Wuchereria</em>;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kodamaea</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Verticillium</em>, or <em>Wuchereria</em>;</p></li>
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -486,8 +486,8 @@
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
<li><p>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on January 8th, 2024.</p></li>
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>

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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -282,7 +282,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt>mic_range</dt>
<dd><p>a manual range to plot the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dt>drop</dt>
@ -334,7 +334,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt>breakpoint_type</dt>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>.</p></dd>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
</dl></div>
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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