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Built site for AMR: 1.8.2.9088@08fe5a8
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9086</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -165,12 +165,12 @@
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<p>With ambiguous user input in <code><a href="as.mo.html">as.mo()</a></code> and all the <code><a href="mo_property.html">mo_*</a></code> functions, the returned results are chosen based on their matching score using <code>mo_matching_score()</code>. This matching score \(m\), is calculated as:</p>
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<p><img src="figures/mo_matching_score.png" width="300" alt="mo matching score"></p>
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<p>where:</p><ul><li><p>\(x\) is the user input;</p></li>
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<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
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<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
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<li><p><i>lev</i> 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 <i>x</i> into <i>n</i>;</p></li>
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<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
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<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
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</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>
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<li><p>\(n\) is a taxonomic name (genus, species, and subspecies);</p></li>
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<li><p>\(l_n\) is the length of \(n\);</p></li>
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<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>
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<li><p>\(p_{n}\) is the human pathogenic prevalence group of \(n\), as described below;</p></li>
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<li><p>\(k_n\) is the taxonomic kingdom of \(n\), set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
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</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>
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) 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>
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<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Reset 17 previously matched input values.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_ESCHR_COLI</span>
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<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Matching scores are based on the resemblance between the input and the full</span>
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<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans according to Bartlett et</span>
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<span class="r-out co"><span class="r-pr">#></span> al. (2022). See ?mo_matching_score.</span>
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<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
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<span class="r-out co"><span class="r-pr">#></span> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span>
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<span class="r-out co"><span class="r-pr">#></span> Based on input "K pneumoniae"</span>
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span>
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<span class="r-out co"><span class="r-pr">#></span> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella</span>
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<span class="r-out co"><span class="r-pr">#></span> palustris (0.333), Kocuria palustris (0.333), Kocuria pelophila</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.333), Kocuria polaris (0.333), Kroppenstedtia pulmonis (0.304),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium phytohabitans (0.282), Kitasatospora putterlickiae</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.269), Kibdelosporangium philippinense (0.266), Kalamiella piersonii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.262), Kitasatospora psammotica (0.260), Kallotenue papyrolyticum</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.250), Kangiella profundi (0.250), Kangsaoukella pontilimi (0.250),</span>
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<span class="r-out co"><span class="r-pr">#></span> Katagnymene pelagic (0.250), Keratinibaculum paraultunense (0.250),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium persicum (0.250), Kitasatoa purpurea (0.250) and</span>
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<span class="r-out co"><span class="r-pr">#></span> Kitasatospora paracochleata (0.250) [showing first 25]</span>
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<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
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<span class="r-out co"><span class="r-pr">#></span> Based on input "E coli"</span>
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span>
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<span class="r-out co"><span class="r-pr">#></span> cloacae (0.571), Ehrlichia canis (0.567), Enterobacter cloacae</span>
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<span class="r-out co"><span class="r-pr">#></span> dissolvens (0.565), Eikenella corrodens (0.553), Erwinia cancerogena</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.553), Enterobacter cloacae (0.550), Enterococcus cecorum (0.550),</span>
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<span class="r-out co"><span class="r-pr">#></span> Ehrlichia chaffeensis (0.548), Enterobacter cancerogena (0.542),</span>
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<span class="r-out co"><span class="r-pr">#></span> Enterobacter cancerogenus (0.540), Ezakiella coagulans (0.484),</span>
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<span class="r-out co"><span class="r-pr">#></span> Effusibacillus consociatus (0.462), Enterococcus crotali (0.433),</span>
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<span class="r-out co"><span class="r-pr">#></span> Erwinia coffeiphila (0.404), Eubacterium coprostanoligenes (0.402),</span>
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<span class="r-out co"><span class="r-pr">#></span> Enterococcus columbae (0.397), Enterococcus camelliae (0.394) and</span>
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<span class="r-out co"><span class="r-pr">#></span> Eubacterium cellulosolvens (0.385) [showing first 25]</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
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<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
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