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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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@@ -92,7 +92,7 @@
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 20 April 2025.</p> generated on 21 April 2025.</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>
@@ -148,21 +148,21 @@ 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">2025-04-20</td> <td align="center">2025-04-21</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">2025-04-20</td> <td align="center">2025-04-21</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">2025-04-20</td> <td align="center">2025-04-21</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>
articles/AMR_for_Python.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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articles/WHONET.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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articles/datasets.html
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@@ -31,7 +31,7 @@
<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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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@@ -81,7 +81,7 @@
<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">20 April 2025</h4> <h4 data-toc-skip class="date">21 April 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>
articles/index.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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articles/welcome_to_AMR.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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authors.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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index.html
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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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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@@ -87,9 +87,8 @@
<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (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>Peer-reviewed, used in over 175 countries, available in 20 languages</li> <li>Peer-reviewed, 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> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
</li> <li>Applies <strong>CLSI 2011-2025</strong> and <strong>EUCAST 2011-2025</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
<li>Applies all recent <strong>CLSI</strong> and <strong>EUCAST</strong> clinical and veterinary breakpoints for MICs, disk zones and ECOFFs</li>
<li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antimicrobial class</li> <li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antimicrobial class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</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>
@@ -114,7 +113,7 @@
</h3> </h3>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p> <p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</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>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>~79,000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2025 and EUCAST 2011-2025 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> and the <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-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 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>
@@ -133,7 +132,7 @@
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span> <code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span>, warn.conflicts <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span> <span></span>
<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><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> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -143,111 +142,27 @@
<span> <span class="co"># antimicrobial selectors:</span></span> <span> <span class="co"># antimicrobial selectors:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antimicrobials.html">all antimicrobials</a> in the <code>AMR</code> package make sure you get what you meant:</p> <span><span class="co">#&gt; [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_fullname()[49m[39m</span></span>
<table class="table"> <span><span class="co">#&gt; [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_is_gram_negative()[49m[39m</span></span>
<thead><tr class="header"> <span><span class="co">#&gt; [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_is_intrinsic_resistant()[49m[39m</span></span>
<th align="left">bacteria</th> <span><span class="co">#&gt; [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m</span></span>
<th align="center">GEN</th> <span><span class="co">#&gt; [34mℹ For [48;5;255mcarbapenems()[49m using columns '[1mIPM[22m' (imipenem) and '[1mMEM[22m' (meropenem)[39m</span></span>
<th align="center">TOB</th> <span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
<th align="center">AMK</th> <span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<th align="center">KAN</th> <span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
<th align="center">IPM</th> <span><span class="co">#&gt; 1 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m </span></span>
<th align="center">MEM</th> <span><span class="co">#&gt; 2 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m </span></span>
</tr></thead> <span><span class="co">#&gt; 3 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m </span></span>
<tbody> <span><span class="co">#&gt; 4 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m</span></span>
<tr class="odd"> <span><span class="co">#&gt; 5 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m</span></span>
<td align="left"><em>Pseudomonas aeruginosa</em></td> <span><span class="co">#&gt; 6 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m</span></span>
<td align="center">I</td> <span><span class="co">#&gt; 7 Stenotrophomonas maltophilia [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m</span></span>
<td align="center">S</td> <span><span class="co">#&gt; 8 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m</span></span>
<td align="center"></td> <span><span class="co">#&gt; 9 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m</span></span>
<td align="center">R</td> <span><span class="co">#&gt; 10 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m</span></span>
<td align="center">S</td> <span><span class="co">#&gt; # ℹ 25 more rows</span></span></code></pre></div>
<td align="center"></td> <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antimicrobials.html">all antimicrobials</a> in the <code>AMR</code> package make sure you get what you meant.</p>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Stenotrophomonas maltophilia</em></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a> <h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
@@ -256,117 +171,119 @@
<p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p> <p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></span></code></pre></div> <span><span class="co">#&gt; [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m</span></span>
<table class="table"> <span><span class="co">#&gt; [34mℹ For [48;5;255mcarbapenems()[49m using columns '[1mIPM[22m' (imipenem) and '[1mMEM[22m' (meropenem)[39m</span></span>
<span><span class="co">#&gt; [31mℹ 502 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m</span></span></code></pre></div>
<table style="width:100%;" class="table">
<colgroup> <colgroup>
<col width="16%">
<col width="14%"> <col width="14%">
<col width="14%"> <col width="14%">
<col width="14%"> <col width="14%">
<col width="10%"> <col width="14%">
<col width="14%">
<col width="14%"> <col width="14%">
<col width="14%"> <col width="14%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Pathogen</th> <th align="left">Pathogen</th>
<th align="center">Amikacin</th> <th align="left">Amikacin</th>
<th align="center">Gentamicin</th> <th align="left">Gentamicin</th>
<th align="center">Imipenem</th> <th align="left">Imipenem</th>
<th align="center">Kanamycin</th> <th align="left">Kanamycin</th>
<th align="center">Meropenem</th> <th align="left">Meropenem</th>
<th align="center">Tobramycin</th> <th align="left">Tobramycin</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS</td> <td align="left">CoNS</td>
<td align="center">0% (0-8%)</td> <td align="left">0% (0-8%,N=43)</td>
<td align="center">86% (82-90%)</td> <td align="left">86% (82-90%,N=309)</td>
<td align="center">52% (37-67%)</td> <td align="left">52% (37-67%,N=48)</td>
<td align="center">0% (0-8%)</td> <td align="left">0% (0-8%,N=43)</td>
<td align="center">52% (37-67%)</td> <td align="left">52% (37-67%,N=48)</td>
<td align="center">22% (12-35%)</td> <td align="left">22% (12-35%,N=55)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>E. coli</em></td> <td align="left">E. coli</td>
<td align="center">100% (98-100%)</td> <td align="left">100% (98-100%,N=171)</td>
<td align="center">98% (96-99%)</td> <td align="left">98% (96-99%,N=460)</td>
<td align="center">100% (99-100%)</td> <td align="left">100% (99-100%,N=422)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">100% (99-100%)</td> <td align="left">100% (99-100%,N=418)</td>
<td align="center">97% (96-99%)</td> <td align="left">97% (96-99%,N=462)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>E. faecalis</em></td> <td align="left">E. faecalis</td>
<td align="center">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="center">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="center">100% (91-100%)</td> <td align="left">100% (91-100%,N=38)</td>
<td align="center">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">0% (0-9%)</td> <td align="left">0% (0-9%,N=39)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>K. pneumoniae</em></td> <td align="left">K. pneumoniae</td>
<td align="center"></td> <td align="left"></td>
<td align="center">90% (79-96%)</td> <td align="left">90% (79-96%,N=58)</td>
<td align="center">100% (93-100%)</td> <td align="left">100% (93-100%,N=51)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">100% (93-100%)</td> <td align="left">100% (93-100%,N=53)</td>
<td align="center">90% (79-96%)</td> <td align="left">90% (79-96%,N=58)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>P. aeruginosa</em></td> <td align="left">P. aeruginosa</td>
<td align="center"></td> <td align="left"></td>
<td align="center">100% (88-100%)</td> <td align="left">100% (88-100%,N=30)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">0% (0-12%)</td> <td align="left">0% (0-12%,N=30)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">100% (88-100%)</td> <td align="left">100% (88-100%,N=30)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>P. mirabilis</em></td> <td align="left">P. mirabilis</td>
<td align="center"></td> <td align="left"></td>
<td align="center">94% (80-99%)</td> <td align="left">94% (80-99%,N=34)</td>
<td align="center">94% (79-99%)</td> <td align="left">94% (79-99%,N=32)</td>
<td align="center"></td> <td align="left"></td>
<td align="center"></td> <td align="left"></td>
<td align="center">94% (80-99%)</td> <td align="left">94% (80-99%,N=34)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>S. aureus</em></td> <td align="left">S. aureus</td>
<td align="center"></td> <td align="left"></td>
<td align="center">99% (97-100%)</td> <td align="left">99% (97-100%,N=233)</td>
<td align="center"></td> <td align="left"></td>
<td align="center"></td> <td align="left"></td>
<td align="center"></td> <td align="left"></td>
<td align="center">98% (92-100%)</td> <td align="left">98% (92-100%,N=86)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. epidermidis</em></td> <td align="left">S. epidermidis</td>
<td align="center">0% (0-8%)</td> <td align="left">0% (0-8%,N=44)</td>
<td align="center">79% (71-85%)</td> <td align="left">79% (71-85%,N=163)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">0% (0-8%)</td> <td align="left">0% (0-8%,N=44)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">51% (40-61%)</td> <td align="left">51% (40-61%,N=89)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>S. hominis</em></td> <td align="left">S. hominis</td>
<td align="center"></td> <td align="left"></td>
<td align="center">92% (84-97%)</td> <td align="left">92% (84-97%,N=80)</td>
<td align="center"></td> <td align="left"></td>
<td align="center"></td> <td align="left"></td>
<td align="center"></td> <td align="left"></td>
<td align="center">85% (74-93%)</td> <td align="left">85% (74-93%,N=62)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. pneumoniae</em></td> <td align="left">S. pneumoniae</td>
<td align="center">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
<td align="center">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
<td align="center"></td> <td align="left"></td>
<td align="center">0% (0-3%)</td> <td align="left">0% (0-3%,N=117)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -374,33 +291,33 @@
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></span></code></pre></div> <span><span class="co">#&gt; [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m</span></span></code></pre></div>
<table style="width:100%;" class="table"> <table class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="25%">
<col width="21%"> <col width="25%">
<col width="33%"> <col width="25%">
<col width="33%"> <col width="25%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Pathogen</th> <th align="left">Pathogen</th>
<th align="center">Piperacillin/tazobactam</th> <th align="left">Piperacillin/tazobactam</th>
<th align="center">Piperacillin/tazobactam + Gentamicin</th> <th align="left">Piperacillin/tazobactam + Gentamicin</th>
<th align="center">Piperacillin/tazobactam + Tobramycin</th> <th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Gram-negative</td> <td align="left">Gram-negative</td>
<td align="center">88% (85-91%)</td> <td align="left">88% (85-91%,N=641)</td>
<td align="center">99% (97-99%)</td> <td align="left">99% (97-99%,N=691)</td>
<td align="center">98% (97-99%)</td> <td align="left">98% (97-99%,N=693)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Gram-positive</td> <td align="left">Gram-positive</td>
<td align="center">86% (82-89%)</td> <td align="left">86% (82-89%,N=345)</td>
<td align="center">98% (96-98%)</td> <td align="left">98% (96-98%,N=1044)</td>
<td align="center">95% (93-97%)</td> <td align="left">95% (93-97%,N=550)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -410,27 +327,33 @@
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span> <span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fl">14</span>,</span> <span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span>
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div> <span><span class="co">#&gt; [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup>
<col width="19%">
<col width="27%">
<col width="26%">
<col width="26%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Збудник</th> <th align="left">Збудник</th>
<th align="center">Гентаміцин</th> <th align="left">Гентаміцин</th>
<th align="center">Тобраміцин</th> <th align="left">Тобраміцин</th>
<th align="center">Ципрофлоксацин</th> <th align="left">Ципрофлоксацин</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Грамнегативні</td> <td align="left">Грамнегативні</td>
<td align="center">96% (95-98%)</td> <td align="left">96% (95-98%,N=684)</td>
<td align="center">96% (94-97%)</td> <td align="left">96% (94-97%,N=686)</td>
<td align="center">91% (88-93%)</td> <td align="left">91% (88-93%,N=684)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Грампозитивні</td> <td align="left">Грампозитивні</td>
<td align="center">63% (60-66%)</td> <td align="left">63% (60-66%,N=1170)</td>
<td align="center">34% (31-38%)</td> <td align="left">34% (31-38%,N=665)</td>
<td align="center">77% (74-80%)</td> <td align="left">77% (74-80%,N=724)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -480,39 +403,13 @@
<span> <span class="co"># and get their 95% confidence intervals using sir_confidence_interval():</span></span> <span> <span class="co"># and get their 95% confidence intervals using sir_confidence_interval():</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
<span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<table class="table"> <span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
<thead><tr class="header"> <span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
<th align="left">ward</th> <span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span>
<th align="center">GEN_total_R</th> <span><span class="co">#&gt; 1 Clinical 0.2289362 0.205-0.254 0.3147503 0.284-0.347 </span></span>
<th align="center">GEN_conf_int</th> <span><span class="co">#&gt; 2 ICU 0.2902655 0.253-0.33 0.4004739 0.353-0.449 </span></span>
<th align="center">TOB_total_R</th> <span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.3676471 0.254-0.493</span></span></code></pre></div>
<th align="center">TOB_conf_int</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="center">0.2289362</td>
<td align="center">0.205-0.254</td>
<td align="center">0.3147503</td>
<td align="center">0.284-0.347</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="center">0.2902655</td>
<td align="center">0.253-0.33</td>
<td align="center">0.4004739</td>
<td align="center">0.353-0.449</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="center">0.2000000</td>
<td align="center">0.131-0.285</td>
<td align="center">0.3676471</td>
<td align="center">0.254-0.493</td>
</tr>
</tbody>
</table>
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p> <p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
@@ -524,137 +421,38 @@
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span> <span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span> <span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">out</span></span></code></pre></div> <span><span class="co">#&gt; [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m</span></span>
<table class="table"> <span><span class="co">#&gt; [34mℹ For [48;5;255mpolymyxins()[49m using column '[1mCOL[22m' (colistin)[39m</span></span>
<thead><tr class="header"> <span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
<th align="left">ward</th> <span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
<th align="right">GEN</th> <span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
<th align="right">TOB</th> <span><span class="co">#&gt; Caused by warning:</span></span>
<th align="right">AMK</th> <span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" ([48;5;255mminimum[49m = 30).</span></span>
<th align="right">KAN</th> <span><span class="va">out</span></span>
<th align="right">COL</th> <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
</tr></thead> <span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>
<tbody> <span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<tr class="odd"> <span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<td align="left">Clinical</td> <span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<td align="right">0.229</td> <span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<td align="right">0.315</td>
<td align="right">0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td align="right">0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td align="right">0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span> <code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span>
<table class="table"> <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<colgroup> <span><span class="co">#&gt; ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
<col width="17%"> <span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<col width="17%"> <span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<col width="17%"> <span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<col width="14%"> <span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<col width="16%">
<col width="16%">
</colgroup>
<thead><tr class="header">
<th align="left">ward</th>
<th align="right">gentamicin</th>
<th align="right">tobramycin</th>
<th>amikacin</th>
<th align="right">kanamycin</th>
<th align="right">colistin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span> <code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div> <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span>
<table class="table"> <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<colgroup> <span><span class="co">#&gt; ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
<col width="17%"> <span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<col width="17%"> <span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<col width="17%"> <span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<col width="14%"> <span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<col width="16%">
<col width="16%">
</colgroup>
<thead><tr class="header">
<th align="left">ward</th>
<th align="right">J01GB03</th>
<th align="right">J01GB01</th>
<th>J01GB06</th>
<th align="right">J01GB04</th>
<th align="right">J01XB01</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
</div> </div>
</div> </div>
<div class="section level3"> <div class="section level3">
@@ -714,7 +512,7 @@
<div class="section level3"> <div class="section level3">
<h3 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a> <h3 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
</h3> </h3>
<p>The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:</p> <p>The initial development of this package was part of, related to, or made possible by the following non-profit organisations and initiatives:</p>
<div align="center"> <div align="center">
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.svg" style="max-width: 200px;"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.svg" style="max-width: 200px;"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.svg" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" style="max-width: 200px;"></a></p> <p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.svg" style="max-width: 200px;"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.svg" style="max-width: 200px;"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.svg" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" style="max-width: 200px;"></a></p>
</div> </div>
news/index.html
+8 -8
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,20 +49,20 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9249" id="amr-2119249">AMR 2.1.1.9249<a class="anchor" aria-label="anchor" href="#amr-2119249"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9250" id="amr-2119250">AMR 2.1.1.9250<a class="anchor" aria-label="anchor" href="#amr-2119250"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p> <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
<div class="section level5"> <div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9249">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9249"></a></h5> <h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9250">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9250"></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’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p> <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="breaking-2-1-1-9249">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9249"></a></h3> <h3 id="breaking-2-1-1-9250">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9250"></a></h3>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li> <ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li> <li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li> <li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="new-2-1-1-9249">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9249"></a></h3> <h3 id="new-2-1-1-9250">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9250"></a></h3>
<ul><li> <ul><li>
<strong>One Health implementation</strong> <strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li> <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@@ -117,7 +117,7 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-1-1-9249">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9249"></a></h3> <h3 id="changed-2-1-1-9250">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9250"></a></h3>
<ul><li>SIR interpretation <ul><li>SIR interpretation
<ul><li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li> <ul><li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li> <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@@ -198,7 +198,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li> <li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="other-2-1-1-9249">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9249"></a></h3> <h3 id="other-2-1-1-9250">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9250"></a></h3>
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org" class="external-link uri">http://amr-for-r.org</a>) will remain to work.</li> <ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org" class="external-link uri">http://amr-for-r.org</a>) will remain to work.</li>
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li> <li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li> <li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@@ -208,7 +208,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li> <li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="older-versions-2-1-1-9249">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9249"></a></h3> <h3 id="older-versions-2-1-1-9250">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9250"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p> <p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li> <ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li> <li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
pkgdown.yml
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@@ -11,7 +11,7 @@ articles:
PCA: PCA.html PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html WHONET: WHONET.html
last_built: 2025-04-20T15:53Z last_built: 2025-04-21T13:41Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles
reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/AMR-options.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/WHONET.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/ab_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
reference/age.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&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 1999-06-30 25 25.80548 0</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.80822 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.22192 31</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.22466 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.37260 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.37534 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.13699 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.13973 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.46575 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.46849 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.17808 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.18082 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.16438 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.16712 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.27397 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.27671 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.64658 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.64932 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.23014 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.23288 21</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
reference/age_groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.av.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.disk.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.mic.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/as.sir.html
+10 -10
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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@@ -827,16 +827,16 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 17</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-20 <span style="color: #949494;">15:54:17</span> 1 DISK ampicillin Strep pneu human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-21 <span style="color: #949494;">13:42:15</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-20 <span style="color: #949494;">15:54:18</span> 1 DISK AMP Escherich… human 20 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-21 <span style="color: #949494;">13:42:16</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-20 <span style="color: #949494;">15:54:18</span> 1 DISK AMP Escherich… human 20 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-21 <span style="color: #949494;">13:42:16</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-20 <span style="color: #949494;">15:54:18</span> 1 DISK GEN Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-21 <span style="color: #949494;">13:42:16</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-20 <span style="color: #949494;">15:54:18</span> 1 DISK TOB Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-21 <span style="color: #949494;">13:42:17</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-20 <span style="color: #949494;">15:54:19</span> 1 MIC AMX B_STRPT_P… human 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-21 <span style="color: #949494;">13:42:17</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-20 <span style="color: #949494;">15:54:19</span> 1 MIC AMX B_STRPT_P… human 0.01 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-21 <span style="color: #949494;">13:42:18</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-20 <span style="color: #949494;">15:54:19</span> 2 MIC AMX B_STRPT_P… human 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-21 <span style="color: #949494;">13:42:18</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-20 <span style="color: #949494;">15:54:19</span> 3 MIC AMX B_STRPT_P… human 4 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-21 <span style="color: #949494;">13:42:18</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
reference/atc_online.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/av_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/av_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/availability.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/clinical_breakpoints.html
+1 -1
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/dosage.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9249</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</small>
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reference/eucast_rules.html
+14 -16
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -130,7 +130,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt> <dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only <code>NA</code> values are modified. To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant.".</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@@ -275,22 +275,20 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="fu">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span> <span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span 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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&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> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv 15</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">eucast_dosage</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">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v10.0 (2020). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&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> ab name standard_dosage high_dosage </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span 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;">2</span> GEN Gentamicin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
</code></pre></div> </code></pre></div>
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reference/microorganisms.html
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reference/mo_matching_score.html
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reference/mo_property.html
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reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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reference/plot.html
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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reference/translate.html
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search.json
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AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. 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AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . 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