mirror of https://github.com/msberends/AMR.git
37 lines
1.9 KiB
R
37 lines
1.9 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mo_matching_score.R
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\name{mo_matching_score}
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\alias{mo_matching_score}
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\title{Calculate the matching score for microorganisms}
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\usage{
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mo_matching_score(x, fullname, uncertainty = 1)
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}
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\arguments{
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\item{x}{Any user input value(s)}
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\item{fullname}{A full taxonomic name, that exists in \code{\link[=microorganisms]{microorganisms$fullname}}}
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\item{uncertainty}{The level of uncertainty set in \code{\link[=as.mo]{as.mo()}}, see \code{allow_uncertain} in that function (here, it defaults to 1, but is automatically determined in \code{\link[=as.mo]{as.mo()}} based on the number of transformations needed to get to a result)}
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}
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\description{
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This helper function is used by \code{\link[=as.mo]{as.mo()}} to determine the most probable match of taxonomic records, based on user input.
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}
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\details{
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The matching score is based on four parameters:
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\enumerate{
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\item A human pathogenic prevalence \eqn{P}, that is categorised into group 1, 2 and 3 (see \code{\link[=as.mo]{as.mo()}});
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\item A kingdom index \eqn{K} is set as follows: Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, and all others = 5;
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\item The level of uncertainty \eqn{U} that is needed to get to a result (1 to 3, see \code{\link[=as.mo]{as.mo()}});
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\item The \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} \eqn{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 \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
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}
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\deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F}
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The final matching score \eqn{M} is calculated as:
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\deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}
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}
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\examples{
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as.mo("E. coli")
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mo_uncertainties()
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}
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