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@ -37,7 +37,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -205,7 +205,7 @@
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 31 May 2024.</p>
generated on 10 June 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-05-31</td>
<td align="center">2024-06-10</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">2024-05-31</td>
<td align="center">2024-06-10</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">2024-05-31</td>
<td align="center">2024-06-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -575,18 +575,18 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co">#&gt; Max. :2019-12-27 </span></span>
<span><span class="co">#&gt; bacteria AMX AMC </span></span>
<span><span class="co">#&gt; Class :mo Class:sir Class:sir </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; Unique:4 %SI :57.1% (n=1549) %SI :63.9% (n=1734) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI - %S :41.0% (n=1112) - %S :52.0% (n=1409) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS - %I :16.1% (n=437) - %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN </span></span>
<span><span class="co">#&gt; &lt;NA&gt; :0 %S :41.0% (n=1112) %S :52.0% (n=1409) </span></span>
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=437) %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %N : 0.0% (n=0) %N : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) TRUE:2712 </span></span>
<span><span class="co">#&gt; %SI :58.0% (n=1574) %SI :62.7% (n=1701) </span></span>
<span><span class="co">#&gt; - %S :51.5% (n=1396) - %S :59.6% (n=1616) </span></span>
<span><span class="co">#&gt; - %I : 6.6% (n=178) - %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; </span></span></code></pre></div>
<span><span class="co">#&gt; %S :51.5% (n=1396) %S :59.6% (n=1616) TRUE:2712 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %N : 0.0% (n=0) %N : 0.0% (n=0)</span></span></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>

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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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articles/datasets.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -194,7 +194,7 @@
<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">31 May 2024</h4>
<h4 data-toc-skip class="date">10 June 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>
@ -526,15 +526,15 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<h2 id="antibiotics-antibiotic-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
</h2>
<p>A data set with 483 rows and 14 columns, containing the following
<p>A data set with 484 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<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 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>It was last updated on 8 June 2024 15:35:25 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original
@ -547,10 +547,10 @@ text file</a> (0.1 MB)<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>
Feather file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
transport (XPT) file</a> (1.5 MB)<br>
@ -1560,8 +1560,8 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em>, and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 January 2023 22:47:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 9 June 2024 09:31:04 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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authors.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="">2.1.1.9037</small>
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index.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">
@ -193,14 +193,15 @@
<a class="anchor" aria-label="anchor" href="#the-amr-package-for-r-"></a>
</h1>
</div>
<p><img src="./endorsement_clsi_eucast.jpg" align="right" height="120"></p>
<ul>
<li>Provides an <strong>all-in-one solution</strong> for AMR data analysis in a One Health approach</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> and data on <strong>all antimicrobial drugs</strong>
<li>Provides the <strong>full microbiological taxonomy</strong> and extensive info on <strong>all antimicrobial drugs</strong>
</li>
<li>Applies all recent <strong>CLSI and EUCAST clinical and veterinary breakpoints</strong> for MICs and disk zones</li>
<li>Corrects for duplicate isolates, <strong>calculates and predicts AMR</strong> per antibiotic class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, and <strong>SNOMED CT</strong>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
</li>
<li>Works on Windows, macOS and Linux with <strong>all versions of R</strong> since R-3.0 and is completely <strong>dependency-free</strong>, highly suitable for places with <strong>limited resources</strong>
</li>
@ -210,7 +211,7 @@
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
</p>
</div>
<hr>
@ -223,7 +224,7 @@
<div class="section level5">
<h5 id="used-in-over-175-countries-translated-into-20-languages">Used in over 175 countries, translated into 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-translated-into-20-languages"></a>
</h5>
<p><a href="./countries_large.png"><img src="./countries.png" target="_blank" align="right" style="max-width: 300px;"></a></p>
<p><a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;"></a></p>
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>

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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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@ -159,18 +159,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9037" id="amr-2119037">AMR 2.1.1.9037<a class="anchor" aria-label="anchor" href="#amr-2119037"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9043" id="amr-2119043">AMR 2.1.1.9043<a class="anchor" aria-label="anchor" href="#amr-2119043"></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 level5">
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9037">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-2-1-1-9037"></a></h5>
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9043">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-2-1-1-9043"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9037">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9037"></a></h3>
<h3 id="breaking-2-1-1-9043">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9043"></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-2-1-1-9037">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9037"></a></h3>
<h3 id="new-2-1-1-9043">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9043"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for 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.</li>
<li>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>.</li>
@ -181,14 +181,17 @@
<code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</li>
</ul></li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now returns additional factor levels “N” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N.</li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “N” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N. Also, to get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (N will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain N and SDD.</li>
<li>The 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 easy 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>
<li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9037">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9037"></a></h3>
<h3 id="changed-2-1-1-9043">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9043"></a></h3>
<ul><li>For SIR interpretation, it is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Extended the antibiotic selectors with <code><a href="../reference/antibiotic_class_selectors.html">nitrofurans()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">rifamycins()</a></code>
</li>
<li>Added “clindamycin inducible screening” as <code>CLI1</code> to the <code>antibiotics</code> data set. Since clindamycin is a lincosamide, the antibiotic selector <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>For MICs:
<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">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
@ -207,9 +210,12 @@
</li>
<li>Fix for mapping ‘high level’ antibiotics in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
<li>When using antibiotic selectors such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using <code>only_treatable = FALSE</code>
</li>
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9037">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9037"></a></h3>
<h3 id="other-2-1-1-9043">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9043"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>
@ -302,7 +308,7 @@
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-2-0-0">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-2-0-0"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI 10.1177/20499361211011373) and Barbieri <em>et al.</em> (2021, DOI 10.1186/s13756-021-00939-2).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>

2
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@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-05-31T19:27Z
last_built: 2024-06-10T08:37Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
reference/AMR-options.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="">2.1.1.9037</small>
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2
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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="">2.1.1.9037</small>
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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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2
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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="">2.1.1.9037</small>
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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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2
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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="">2.1.1.9037</small>
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2
reference/add_custom_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="">2.1.1.9037</small>
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2
reference/add_custom_microorganisms.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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
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22
reference/age.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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">
@ -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 58.48634 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.24863 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.57923 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.29235 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.27869 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.38798 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.75956 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.34426 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.95355 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.80601 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.51366 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.27596 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.60656 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.31967 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.30601 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.41530 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.78689 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.37158 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.98087 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.83333 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -200,22 +200,26 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<span></span>
<span><span class="fu">glycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">lincosamides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">lincosamides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">lipoglycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">macrolides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">nitrofurans</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">oxazolidinones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">penicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">polymyxins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">streptogramins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">quinolones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">rifamycins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">streptogramins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">tetracyclines</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">trimethoprims</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
@ -299,13 +303,15 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)</p></li>
<li><p><code>lincosamides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)</p></li>
<li><p><code>lincosamides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), clindamycin inducible screening (CLI1), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>
<li><p><code>macrolides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)</p></li>
<li><p><code>nitrofurans()</code> can select: <br> furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)</p></li>
<li><p><code>oxazolidinones()</code> can select: <br> cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>polymyxins()</code> can select: <br> colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>rifamycins()</code> can select: <br> rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)</p></li>
<li><p><code>streptogramins()</code> can select: <br> pristinamycin (PRI) and quinupristin/dalfopristin (QDA)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)</p></li>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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
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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">

22
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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">
@ -244,7 +244,10 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "disk", method_long = "disk diffusion zones", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = FALSE, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = NULL, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</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> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">df</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
@ -252,7 +255,20 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "disk", method_long = "disk diffusion zones", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = FALSE, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = NULL, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'AMP' (ampicillin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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> Interpreting disk diffusion zones: column 'CIP' (ciprofloxacin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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">
@ -291,7 +291,12 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Meningitis'.</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</span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -1,12 +1,12 @@
<!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="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.
<!-- 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 containing the levels S, SDD, I, R, N.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
All breakpoints used for interpretation are available in our 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/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/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/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></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.
All breakpoints used for interpretation are available in our 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/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/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/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></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 containing the levels S, SDD, I, R, N.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -174,7 +174,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
</div>
<div class="ref-description section level2">
<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>.</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> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>N</code>.</p>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
@ -195,10 +195,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span><span class="fu">as.sir</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
<span> I <span class="op">=</span> <span class="st">"^(I|H)+$"</span>,</span>
<span> I <span class="op">=</span> <span class="st">"^(I)+$"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
<span> N <span class="op">=</span> <span class="st">"^(N|V)+$"</span>,</span>
<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D)+$"</span>,</span>
<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -276,7 +276,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt>S, I, R, N, SDD</dt>
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters are removed from the input.</p></dd>
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
<dt>mo</dt>
@ -405,7 +405,8 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
</div>
<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
@ -467,102 +468,102 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> Max. :2017-12-28 Max. :97.00 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward mo PEN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Length:2000 Class :mo Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class :character &lt;NA&gt; :0 %R :73.7% (n=1201) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Mode :character Unique:90 %SI :26.3% (n=428) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class :character &lt;NA&gt; :0 %S :25.6% (n=417) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :68.8% (n=251) %SI :70.5% (n=665) %SI :40.4% (n=546) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :68.8% (n=251) - %S :70.5% (n=665) - %S :40.2% (n=543) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.2% (n=3) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMC AMP TZP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :76.3% (n=1433) %SI :40.4% (n=546) %SI :87.4% (n=875) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :71.4% (n=1342) - %S :40.2% (n=543) - %S :86.1% (n=862) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 4.8% (n=91) - %I : 0.2% (n=3) - %I : 1.3% (n=13) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CZO FEP CXM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :55.4% (n=247) %SI :85.8% (n=621) %SI :73.7% (n=1319) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :54.9% (n=245) - %S :85.6% (n=620) - %S :72.5% (n=1297) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.4% (n=2) - %I : 0.1% (n=1) - %I : 1.2% (n=22) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FOX CTX CAZ </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :72.6% (n=594) %SI :84.5% (n=797) %SI :33.5% (n=607) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :71.6% (n=586) - %S :84.4% (n=796) - %S :33.5% (n=607) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 1.0% (n=8) - %I : 0.1% (n=1) - %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CRO GEN TOB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :84.5% (n=797) %SI :75.4% (n=1399) %SI :65.6% (n=886) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :84.4% (n=796) - %S :74.0% (n=1372) - %S :65.1% (n=879) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.1% (n=1) - %I : 1.5% (n=27) - %I : 0.5% (n=7) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMK KAN TMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :36.3% (n=251) %SI : 0.0% (n=0) %SI :61.9% (n=928) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :36.3% (n=251) - %S : 0.0% (n=0) - %S :61.2% (n=918) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.7% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SXT NIT FOS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :79.5% (n=1398) %SI :82.9% (n=616) %SI :57.8% (n=203) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :79.1% (n=1392) - %S :76.0% (n=565) - %S :57.8% (n=203) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.3% (n=6) - %I : 6.9% (n=51) - %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> LNZ CIP MFX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :30.7% (n=314) %SI :83.8% (n=1181) %SI :66.4% (n=140) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :30.7% (n=314) - %S :78.9% (n=1112) - %S :64.5% (n=136) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 4.9% (n=69) - %I : 1.9% (n=4) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> VAN TEC TCY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :61.7% (n=1149) %SI :24.3% (n=237) %SI :70.3% (n=843) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :61.7% (n=1149) - %S :24.3% (n=237) - %S :68.3% (n=820) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 1.9% (n=23) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TGC DOX ERY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :87.3% (n=697) %SI :72.3% (n=821) %SI :42.8% (n=810) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :87.3% (n=697) - %S :71.7% (n=814) - %S :42.3% (n=801) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 0.6% (n=7) - %I : 0.5% (n=9) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CLI AZM IPM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :38.8% (n=590) %SI :42.8% (n=810) %SI :93.8% (n=834) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :38.6% (n=586) - %S :42.3% (n=801) - %S :92.7% (n=824) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.3% (n=4) - %I : 0.5% (n=9) - %I : 1.1% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> MEM MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :94.1% (n=780) %SI :85.3% (n=29) %SI :78.6% (n=121) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :94.1% (n=780) - %S :85.3% (n=29) - %S :78.6% (n=121) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> COL MUP RIF </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SI :18.8% (n=309) %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %S :18.8% (n=309) - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> - %I : 0.0% (n=0) - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
<span class="r-in"><span></span></span>
@ -580,17 +581,41 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</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> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</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: 4 × 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;mo&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> 2024-05-31 <span style="color: #949494;">19:28:05</span> 1 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 0.01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 2 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 3 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2024-05-31 <span style="color: #949494;">19:28:05</span> 4 AMX B_STRPT_PNMN AMX B_STRPT_PNMN 8 </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> 2024-06-10 <span style="color: #949494;">08:38:18</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> 2024-06-10 <span style="color: #949494;">08:38:18</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> 2024-06-10 <span style="color: #949494;">08:38:17</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> 2024-06-10 <span style="color: #949494;">08:38:17</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:13</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> 2024-06-10 <span style="color: #949494;">08:38:12</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> 2024-06-10 <span style="color: #949494;">08:38:12</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>
@ -605,7 +630,12 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Non-meningitis'.</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</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
@ -617,7 +647,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "disk", method_long = "disk diffusion zones", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = FALSE, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = NULL, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</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> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
@ -661,12 +694,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
@ -685,12 +712,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
@ -703,12 +724,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(where(is.mic), as.sir)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
@ -727,12 +742,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
@ -751,12 +760,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(AMP:TOB, as.sir)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
@ -775,17 +778,41 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `AMP = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in as_sir_method(method_short = "mic", method_long = "MIC values", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = conserve_capped_values, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = host, ...):</span> object 'mo_var_found' not found</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.sir(uti = FALSE) to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</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> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</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> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</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> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</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 &lt;NA&gt; S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
@ -805,6 +832,13 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot</a></span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
<span class="r-plt img"><img src="as.sir-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 4 5 NA</span>
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 2 3 NA NA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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
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="">2.1.1.9037</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9043</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
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@ -10,7 +10,7 @@
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reference/availability.html
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@ -10,7 +10,7 @@
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reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
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reference/clinical_breakpoints.html
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@ -16,7 +16,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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@ -246,7 +246,7 @@
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 28 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<p>These 30 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
<li><p>antifungals<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
@ -262,13 +262,15 @@
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>glycopeptides<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>lincosamides<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>lincosamides<br>(acetylmidecamycin, acetylspiramycin, clindamycin, clindamycin inducible screening, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>lipoglycopeptides<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>macrolides<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>nitrofurans<br>(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)</p></li>
<li><p>oxazolidinones<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>penicillins<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>polymyxins<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>rifamycins<br>(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)</p></li>
<li><p>streptogramins<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, and tetracycline)</p></li>

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@ -10,7 +10,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Export Data Set as NCBI BioSample Antibiogram</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/export_biosample.R" class="external-link"><code>R/export_biosample.R</code></a></small>
<div class="d-none name"><code>export_ncbi_biosample.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Export Data Set as NCBI BioSample Antibiogram</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">export_ncbi_biosample</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"biosample_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"%Y-%m-%d-%H%M%S"</span><span class="op">)</span>, <span class="st">".xlsx"</span><span class="op">)</span>,</span>
<span> type <span class="op">=</span> <span class="st">"pathogen MIC"</span>,</span>
<span> columns <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span>
<span> save_as_xlsx <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a data set</p></dd>
<dt>filename</dt>
<dd><p>a character string specifying the file name</p></dd>
<dt>type</dt>
<dd><p>a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/" class="external-link">https://www.ncbi.nlm.nih.gov/biosample/docs/</a></p></dd>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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</dt>
<dd>Add Custom Antimicrobials</dd>
</dl></div><div class="section level2">
<h2 id="preparing-data">Preparing data<a class="anchor" aria-label="anchor" href="#preparing-data"></a></h2>
<h2 id="preparing-data-antimicrobial-results">Preparing data: antimicrobial results<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-results"></a></h2>
<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></div>
@ -329,7 +329,7 @@
<dd>Determine Bug-Drug Combinations</dd>
</dl><dl><dt>
<code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">ab_selector()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">aminopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">antifungals()</a></code> <code><a href="antibiotic_class_selectors.html">antimycobacterials()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">lincosamides()</a></code> <code><a href="antibiotic_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">polymyxins()</a></code> <code><a href="antibiotic_class_selectors.html">streptogramins()</a></code> <code><a href="antibiotic_class_selectors.html">quinolones()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> <code><a href="antibiotic_class_selectors.html">trimethoprims()</a></code> <code><a href="antibiotic_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_per_os()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_iv()</a></code> <code><a href="antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>
<code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">ab_selector()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">aminopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">antifungals()</a></code> <code><a href="antibiotic_class_selectors.html">antimycobacterials()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">lincosamides()</a></code> <code><a href="antibiotic_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">nitrofurans()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">polymyxins()</a></code> <code><a href="antibiotic_class_selectors.html">quinolones()</a></code> <code><a href="antibiotic_class_selectors.html">rifamycins()</a></code> <code><a href="antibiotic_class_selectors.html">streptogramins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> <code><a href="antibiotic_class_selectors.html">trimethoprims()</a></code> <code><a href="antibiotic_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_per_os()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_iv()</a></code> <code><a href="antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>
</dt>
<dd>Antibiotic Selectors</dd>
</dl><dl><dt>
@ -374,7 +374,7 @@
</dt>
<dd>PCA Biplot with <code>ggplot2</code></dd>
</dl></div><div class="section level2">
<h2 id="other-amr-specific-options">Other: AMR-specific options<a class="anchor" aria-label="anchor" href="#other-amr-specific-options"></a></h2>
<h2 id="amr-specific-options">AMR-specific options<a class="anchor" aria-label="anchor" href="#amr-specific-options"></a></h2>
<div class="section-desc"><p>The AMR package is customisable, by providing settings that can be set per user or per team. For example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported language can be set for the whole team (system-language independent) for antibiotic names in a foreign language.</p></div>
@ -450,7 +450,7 @@
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
</dt>
<dd>Data Sets with 603 Antimicrobial Drugs</dd>
<dd>Data Sets with 604 Antimicrobial Drugs</dd>
</dl><dl><dt>
<code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code>
@ -504,6 +504,11 @@
<dd>Age in Years of Individuals</dd>
</dl><dl><dt>
<code><a href="export_ncbi_biosample.html">export_ncbi_biosample()</a></code>
</dt>
<dd>Export Data Set as NCBI BioSample Antibiogram</dd>
</dl><dl><dt>
<code><a href="availability.html">availability()</a></code>
</dt>
<dd>Check Availability of Columns</dd>

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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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@ -10,7 +10,7 @@
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reference/plot.html
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/resistance_predict.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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