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(v1.7.1.9069) CLSI 2021 support

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dr. M.S. (Matthijs) Berends
2021-12-12 11:36:58 +01:00
parent 1e66a3daf3
commit f90e27c1b0
30 changed files with 10419 additions and 6927 deletions
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8
docs/reference/as.rsi.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9069</span>
</span>
</div>
@ -261,8 +261,8 @@
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2020"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2021"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
</div>
<div class="section">
@ -276,7 +276,7 @@
<h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 23,451 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">

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docs/reference/index.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9069</span>
</span>
</div>

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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9069</span>
</span>
</div>
@ -177,7 +177,7 @@
<span class="op">)</span>
<span class="co"># S3 method for mic</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
ab <span class="op">=</span> <span class="cn">NULL</span>,
@ -192,7 +192,7 @@
<span class="op">)</span>
<span class="co"># S3 method for mic</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu">plot</span><span class="op">(</span>
@ -210,7 +210,7 @@
<span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
ab <span class="op">=</span> <span class="cn">NULL</span>,
@ -225,7 +225,7 @@
<span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu">plot</span><span class="op">(</span>
@ -237,7 +237,7 @@
<span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Overview of"</span>, <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
xlab <span class="op">=</span> <span class="st">"Antimicrobial Interpretation"</span>,
@ -248,7 +248,7 @@
<span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<div id="arguments">
<h2>Arguments</h2>
@ -281,7 +281,7 @@ The <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="
<div id="details">
<h2>Details</h2>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
</div>
<div id="stable-lifecycle">

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<!DOCTYPE html>
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9069</span>
</span>
</div>
@ -158,14 +158,14 @@
</div>
<div class="ref-description">
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div></div>
<div id="format">
<h2>Format</h2>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 22,000 observations and 10 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 23,451 observations and 10 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>