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<spanclass="co">#> NOTE: Using column 'mo' as input for mo_is_gram_negative()</span>
<spanclass="co">#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
<spanclass="co">#> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
@ -229,7 +270,7 @@
<spanclass="co">#> 'KAN' (kanamycin) and 'TOB' (tobramycin)</span>
<spanclass="co">#> Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><ahref="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><ahref="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><ahref="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <ahref="./reference/microorganisms.html">all microorganisms</a> and <ahref="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<tableclass="table">
<table>
<thead><trclass="header">
<thalign="left">bacteria</th>
<thalign="center">AMK</th>
@ -391,7 +432,7 @@
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<codeclass="sourceCode R"><spanclass="fu"><ahref="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><spanclass="op">(</span><spanclass="st">"remotes"</span><spanclass="op">)</span><spanclass="co"># if you haven't already</span>
<p>You can also download the latest build from our repository: <ahref="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz"class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
</div>
</div>
@ -453,7 +494,7 @@
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code><ahref="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></code>)</li>
<li>Plot AMR results with <code><ahref="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><ahref="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
<ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a><br><smallclass="roles"> Author, maintainer </small><ahref="https://orcid.org/0000-0001-7620-1800"target="orcid.widget"aria-label="ORCID"><spanclass="fab fa-orcid orcid"aria-hidden="true"></span></a></li>
<li>
<ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a><br><smallclass="roles"> Author, contributor </small><ahref="https://orcid.org/0000-0001-5809-5995"target="orcid.widget"aria-label="ORCID"><spanclass="fab fa-orcid orcid"aria-hidden="true"></span></a></li>
<li>
<ahref="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a><br><smallclass="roles"> Author, thesis advisor </small><ahref="https://orcid.org/0000-0003-4881-038X"target="orcid.widget"aria-label="ORCID"><spanclass="fab fa-orcid orcid"aria-hidden="true"></span></a></li>
<li>
<ahref="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a><br><smallclass="roles"> Author, thesis advisor </small><ahref="https://orcid.org/0000-0003-1634-0010"target="orcid.widget"aria-label="ORCID"><spanclass="fab fa-orcid orcid"aria-hidden="true"></span></a></li>
<li>
<ahref="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a><br><smallclass="roles"> Author, thesis advisor </small><ahref="https://orcid.org/0000-0002-9213-6743"target="orcid.widget"aria-label="ORCID"><spanclass="fab fa-orcid orcid"aria-hidden="true"></span></a></li>
<p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <ahref="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <ahref="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <ahref="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <ahref="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<footer>
<divclass="copyright">
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9042</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9043</span>
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