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<img src="../logo.svg" class="logo" alt=""><h1>Calculate the Matching Score for Microorganisms</h1>
<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>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/mo_matching_score.R" class="external-link"><code>R/mo_matching_score.R</code></a></small>
<div class="d-none name"><code>mo_matching_score.Rd</code></div>
</div>
@@ -170,11 +64,13 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Any user input value(s)</p></dd>
<dt>n</dt>
<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
</dl></div>
@@ -187,7 +83,7 @@
</div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
<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>
<p><img src="figures/mo_matching_score.png" width="300" alt="mo matching score"></p>
@@ -203,14 +99,14 @@
</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>
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kodamaea</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Verticillium</em>, or <em>Wuchereria</em>;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Verticillium</em>, or <em>Wuchereria</em>;</p></li>
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<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> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -233,12 +129,12 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> --------------------------------------------------------------------------------</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Escherichia coli coli (0.643), Escherichia coli</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> expressing (0.611), Enterobacter cowanii (0.600), Eubacterium combesii</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> cloacae (0.571), Enterobacter cloacae complex (0.571), and Ehrlichia</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> canis (0.567)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.583), Enterococcus casseliflavus (0.577), and Enterobacter cloacae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> cloacae (0.571)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Only the first 10 other matches of each record are shown. Run</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
@@ -251,7 +147,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6875000 0.3809524</span>
</code></pre></div>
</div>
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@@ -265,9 +161,9 @@
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