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<img src="../logo.svg" class="logo" alt=""><h1>Calculate the Matching Score for Microorganisms</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mo_matching_score.R" class="external-link"><code>R/mo_matching_score.R</code></a></small>
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<div class="d-none name"><code>mo_matching_score.Rd</code></div>
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<p>This algorithm is used by <code><a href="as.mo.html">as.mo()</a></code> and all the <code><a href="mo_property.html">mo_*</a></code> functions to determine the most probable match of taxonomic records based on user input.</p>
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></span></code></pre></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>Any user input value(s)</p></dd>
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<dt>n</dt>
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<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
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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><i>x</i> 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>, which counts any insertion, deletion and substitution as 1 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 experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
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<p>All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<div class="section level2">
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<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
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<p>Dr Matthijs Berends</p>
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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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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</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 pathogenicity in humans and the resemblance</span>
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<span class="r-out co"><span class="r-pr">#></span> between the input and the full taxonomic name. 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> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Entamoeba coli (0.079)</span>
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<span class="r-out co"><span class="r-pr">#></span> </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>x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
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<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</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> [1] 0.68750000 0.07936508</span>
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</code></pre></div>
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