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< 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 >
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< 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 >
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< p > $$L' = 1 - \frac{0.5L}{F}$$< / p >
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< p > The final matching score \(M\) is calculated as:
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$$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$< / p >
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< 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 > ()
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< 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 >
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