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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9013</small>
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Conduct AMR Analysis
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Predict Antimicrobial Resistance
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AMR &amp; dplyr/tidyverse
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<h3>All vignettes</h3>
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<dl><dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
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</dd><dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
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</dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
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</dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
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</dd><dt><a href="other_pkg.html">Using AMR with other packages: AMR &amp; dplyr/tidyverse</a></dt>
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</dd><dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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