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<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the matching score for microorganisms</h1> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_matching_score.R'><code>R/mo_matching_score.R</code></a></small> <div class="hidden name"><code>mo_matching_score.Rd</code></div> </div> <div class="ref-description"> <p>This helper function is used by <code><a href='as.mo.html'>as.mo()</a></code> to determine the most probable match of taxonomic records, based on user input.</p> </div> <pre class="usage"><span class='fu'>mo_matching_score</span>(<span class='kw'>x</span>, <span class='kw'>fullname</span>, uncertainty = <span class='fl'>1</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>x</th> <td><p>Any user input value(s)</p></td> </tr> <tr> <th>fullname</th> <td><p>A full taxonomic name, that exists in <code><a href='microorganisms.html'>microorganisms$fullname</a></code></p></td> </tr> <tr> <th>uncertainty</th> <td><p>The level of uncertainty set in <code><a href='as.mo.html'>as.mo()</a></code>, see <code>allow_uncertain</code> in that function (here, it defaults to 1, but is automatically determined in <code><a href='as.mo.html'>as.mo()</a></code> based on the number of transformations needed to get to a result)</p></td> </tr> </table> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The matching score is based on four parameters:</p><ol> <li><p>A human pathogenic prevalence \(P\), that is categorised into group 1, 2 and 3 (see <code><a href='as.mo.html'>as.mo()</a></code>);</p></li> <li><p>A kingdom index \(K\) is set as follows: Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, and all others = 5;</p></li> <li><p>The level of uncertainty \(U\) that is needed to get to a result (1 to 3, see <code><a href='as.mo.html'>as.mo()</a></code>);</p></li> <li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li> </ol> <p>$$L' = 1 - \frac{0.5L}{F}$$</p> <p>The final matching score \(M\) is calculated as: $$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>) <span class='fu'><a href='as.mo.html'>mo_uncertainties</a></span>() </pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> <h2 data-toc-skip>Contents</h2> </nav> </div> </div> <footer> <div class="copyright"> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p> </div> </footer> </div> </body> </html>