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dr. M.S. (Matthijs) Berends
2023-01-06 19:21:04 +01:00
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commit 84ed8c32bb
12 changed files with 37 additions and 64 deletions
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R/mo_matching_score.R
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@ -30,7 +30,7 @@
#' Calculate the Matching Score for Microorganisms
#'
#' This algorithm is used by [as.mo()] and all the [`mo_*`][mo_property()] functions to determine the most probable match of taxonomic records based on user input.
#' @author Dr. Matthijs Berends
#' @author Dr. Matthijs Berends, 2018
#' @param x Any user input value(s)
#' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
#' @note This algorithm was originally described in: Berends MS *et al.* (2022). **AMR: An R Package for Working with Antimicrobial Resistance Data**. *Journal of Statistical Software*, 104(3), 1-31; \doi{10.18637/jss.v104.i03}.
@ -43,7 +43,7 @@
#'
#' where:
#'
#' * \ifelse{html}{\out{<i>x</i> is the user input;}}{\eqn{x} is the user input;}
#' * \eqn{x} is the user input;
#' * \ifelse{html}{\out{<i>n</i> is a taxonomic name (genus, species, and subspecies);}}{\eqn{n} is a taxonomic name (genus, species, and subspecies);}
#' * \ifelse{html}{\out{<i>l<sub>n</sub></i> is the length of <i>n</i>;}}{l_n is the length of \eqn{n};}
#' * \ifelse{html}{\out{<i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;}}{lev is the Levenshtein distance function (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};}