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Built site for AMR: 1.8.2.9092@ca79068

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<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="">1.8.2.9091</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
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<li><p>\(n\) is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p>\(l_n\) is the length of \(n\);</p></li>
<li><p>\(lev\) is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \(x\) into \(n\);</p></li>
<li><p>\(p_{n}\) is the human pathogenic prevalence group of \(n\), as described below;</p></li>
<li><p>\(p_n\) is the human pathogenic prevalence group of \(n\), as described below;</p></li>
<li><p>\(k_n\) is the taxonomic kingdom of \(n\), set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
</ul><p>The grouping into human pathogenic prevalence \(p\) is based on recent work from Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>