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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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website update since they are based on randomly created values and the 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 15 June 2024.</p> generated on 16 June 2024.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2024-06-15</td> <td align="center">2024-06-16</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2024-06-15</td> <td align="center">2024-06-16</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2024-06-15</td> <td align="center">2024-06-16</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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@ -194,7 +194,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">15 June 2024</h4> <h4 data-toc-skip class="date">16 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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>
@ -2176,11 +2176,11 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
<h2 id="microorganisms-codes-common-laboratory-codes"> <h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a> <code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2> </h2>
<p>A data set with 4 972 rows and 2 columns, containing the following <p>A data set with 4 971 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p> column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>, <p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p> after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info <p>It was last updated on 16 June 2024 09:28:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p> about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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@ -194,8 +194,8 @@
</h1> </h1>
</div> </div>
<ul> <ul>
<li>Provides an <strong>all-in-one solution</strong> for AMR data analysis in a One Health approach</li> <li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
<li>Used in over 175 countries, translated into 20 languages</li> <li>Used in over 175 countries, available in 20 languages</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li> <li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> and extensive info 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>
@ -223,7 +223,7 @@
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p> <p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p> <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level5"> <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 id="used-in-over-175-countries-available-in-20-languages">Used in over 175 countries, available in 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-20-languages"></a>
</h5> </h5>
<p><a href="./countries_large.png" target="_blank"><img src="./countries.png" 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>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>

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -159,18 +159,18 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9050" id="amr-2119050">AMR 2.1.1.9050<a class="anchor" aria-label="anchor" href="#amr-2119050"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9051" id="amr-2119051">AMR 2.1.1.9051<a class="anchor" aria-label="anchor" href="#amr-2119051"></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> <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"> <div class="section level5">
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9050">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-2-1-1-9050"></a></h5> <h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9051">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-2-1-1-9051"></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> <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>
<div class="section level3"> <div class="section level3">
<h3 id="breaking-2-1-1-9050">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9050"></a></h3> <h3 id="breaking-2-1-1-9051">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9051"></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><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> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="new-2-1-1-9050">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9050"></a></h3> <h3 id="new-2-1-1-9051">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9051"></a></h3>
<ul><li>One Health implementation <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> <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> <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>
@ -188,7 +188,7 @@
<li>Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.</li> <li>Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-1-1-9050">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9050"></a></h3> <h3 id="changed-2-1-1-9051">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9051"></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> <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>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>
@ -221,7 +221,7 @@
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li> <li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="other-2-1-1-9050">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9050"></a></h3> <h3 id="other-2-1-1-9051">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9051"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li> <ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div> </ul></div>
</div> </div>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html WHONET: WHONET.html
last_built: 2024-06-15T13:37Z last_built: 2024-06-16T09:32Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
reference/AMR-options.html
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@ -10,7 +10,7 @@
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reference/AMR.html
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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reference/WHOCC.html
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@ -10,7 +10,7 @@
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reference/ab_from_text.html
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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2
reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
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reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
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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> <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="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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@ -222,16 +222,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</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 58.52732 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.53005 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.28962 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.29235 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.62022 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.62295 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.33333 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.33607 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.31967 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.32240 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.42896 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.43169 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.80055 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.80328 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.38525 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.38798 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.99454 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.99727 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.84699 13</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.84973 13</span>
</code></pre></div> </code></pre></div>
</div> </div>
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -649,19 +649,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 15</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 15</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo method</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo method</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;chr&gt;</span> </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;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN DISK </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 8 more variables: input &lt;dbl&gt;, outcome &lt;sir&gt;, host &lt;chr&gt;, notes &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 8 more variables: input &lt;dbl&gt;, outcome &lt;sir&gt;, host &lt;chr&gt;, notes &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;, breakpoint_S_R &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>

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reference/atc_online.html
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@ -10,7 +10,7 @@
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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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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@ -12,7 +12,7 @@
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<code><a href="microorganisms.codes.html">microorganisms.codes</a></code> <code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt> </dt>
<dd>Data Set with 4 972 Common Microorganism Codes</dd> <dd>Data Set with 4 971 Common Microorganism Codes</dd>
</dl><dl><dt> </dl><dl><dt>
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code> <code><a href="microorganisms.groups.html">microorganisms.groups</a></code>

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</nav><div class="container template-reference-topic"> </nav><div class="container template-reference-topic">
<div class="row"> <div class="row">
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 972 Common Microorganism Codes</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 971 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.codes.Rd</code></div> <div class="d-none name"><code>microorganisms.codes.Rd</code></div>
</div> </div>
@ -170,7 +170,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 972 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em>This is a unique identifier.</em></p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 971 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em>This is a unique identifier.</em></p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li> <li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
@ -185,7 +185,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,972 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,971 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span> <span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011 B_GRAMP </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011 B_GRAMP </span>
@ -198,7 +198,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 B_STRPT </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 B_STRPT </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,962 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,961 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span> <span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>

2
reference/microorganisms.groups.html
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@ -10,7 +10,7 @@
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reference/microorganisms.html
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@ -10,7 +10,7 @@
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reference/mo_matching_score.html
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@ -10,7 +10,7 @@
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reference/mo_property.html
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@ -10,7 +10,7 @@
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reference/mo_source.html
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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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reference/pca.html
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9051</small>
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2
reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -10,7 +10,7 @@
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reference/resistance_predict.html
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@ -10,7 +10,7 @@
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reference/skewness.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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reference/translate.html
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search.json
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