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new species groups, updated clinical breakpoints

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dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
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10
R/mo_matching_score.R
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# ==================================================================== #
# TITLE #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
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#' * \eqn{l_n} is the length of \eqn{n};
#' * \eqn{lev} is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance) (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
#' * \eqn{p_n} is the human pathogenic prevalence group of \eqn{n}, as described below;
#' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.
#' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Archaea = 2, others = 3.
#'
#' The grouping into human pathogenic prevalence \eqn{p} is based on recent work from Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:
#'
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#' - Any genus present in the **established** list also has `prevalence = 1.0` in the [microorganisms] data set;
#' - Any other genus present in the **putative** list has `prevalence = 1.25` in the [microorganisms] data set;
#' - Any other species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 1.5` in the [microorganisms] data set;
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.5` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`;
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.25` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`;
#' - All other records have `prevalence = 2.0` in the [microorganisms] data set.
#'
#' When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.