AMR/man/mo_matching_score.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo_matching_score.R
\name{mo_matching_score}
\alias{mo_matching_score}
\title{Calculate the matching score for microorganisms}
\usage{
mo_matching_score(x, fullname, uncertainty = 1)
}
\arguments{
\item{x}{Any user input value(s)}

\item{fullname}{A full taxonomic name, that exists in \code{\link[=microorganisms]{microorganisms$fullname}}}

\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)}
}
\description{
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.
}
\details{
The matching score is based on four parameters:
\enumerate{
\item A human pathogenic prevalence \eqn{P}, that is categorised into group 1, 2 and 3 (see \code{\link[=as.mo]{as.mo()}});
\item A kingdom index \eqn{K} is set as follows: Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, and all others = 5;
\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()}});
\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:
}

\deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}

The final matching score \eqn{M} is calculated as:
\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)}
}
\examples{
as.mo("E. coli")
mo_uncertainties()
}