mirror of https://github.com/msberends/AMR.git
119 lines
7.6 KiB
R
Executable File
119 lines
7.6 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# CITE 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. #
|
|
# doi:10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' 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
|
|
#' @param x Any user input value(s)
|
|
#' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
|
|
#' @note This algorithm was 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}.
|
|
#' @section Matching Score for Microorganisms:
|
|
#' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, is calculated as:
|
|
#'
|
|
#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
|
#'
|
|
#' where:
|
|
#'
|
|
#' * \ifelse{html}{\out{<i>x</i> 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};}
|
|
#' * \ifelse{html}{\out{<i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;}}{p_n is the human pathogenic prevalence group of \eqn{n}, as described below;}
|
|
#' * \ifelse{html}{\out{<i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
|
|
#'
|
|
#' The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:
|
|
#'
|
|
#' **Group 1** (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacterales.
|
|
#'
|
|
#' **Group 2** consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`.
|
|
#'
|
|
#' **Group 3** consists of all other microorganisms.
|
|
#'
|
|
#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
|
|
#'
|
|
#' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
|
#' @export
|
|
#' @inheritSection AMR Reference Data Publicly Available
|
|
#' @examples
|
|
#' as.mo("E. coli")
|
|
#' mo_uncertainties()
|
|
#'
|
|
#' mo_matching_score(
|
|
#' x = "E. coli",
|
|
#' n = c("Escherichia coli", "Entamoeba coli")
|
|
#' )
|
|
mo_matching_score <- function(x, n) {
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list"))
|
|
meet_criteria(n, allow_class = "character")
|
|
|
|
x <- parse_and_convert(x)
|
|
# no dots and other non-whitespace characters
|
|
x <- gsub("[^a-zA-Z0-9 \\(\\)]+", "", x)
|
|
|
|
# only keep one space
|
|
x <- gsub(" +", " ", x)
|
|
|
|
# force a capital letter, so this conversion will not count as a substitution
|
|
substr(x, 1, 1) <- toupper(substr(x, 1, 1))
|
|
|
|
# n is always a taxonomically valid full name
|
|
if (length(n) == 1) {
|
|
n <- rep(n, length(x))
|
|
}
|
|
if (length(x) == 1) {
|
|
x <- rep(x, length(n))
|
|
}
|
|
|
|
# length of fullname
|
|
l_n <- nchar(n)
|
|
lev <- double(length = length(x))
|
|
l_n.lev <- double(length = length(x))
|
|
lev <- unlist(Map(f = function(a, b) {
|
|
as.double(utils::adist(a, b,
|
|
ignore.case = FALSE,
|
|
fixed = TRUE,
|
|
costs = c(insertions = 1, deletions = 2, substitutions = 2),
|
|
counts = FALSE
|
|
))
|
|
}, x, n, USE.NAMES = FALSE))
|
|
|
|
l_n.lev[l_n < lev] <- l_n[l_n < lev]
|
|
l_n.lev[lev < l_n] <- lev[lev < l_n]
|
|
l_n.lev[lev == l_n] <- lev[lev == l_n]
|
|
|
|
# human pathogenic prevalence (1 to 3), see ?as.mo
|
|
p_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "prevalence", drop = TRUE]
|
|
# kingdom index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
|
|
k_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "kingdom_index", drop = TRUE]
|
|
|
|
# matching score:
|
|
(l_n - 0.5 * l_n.lev) / (l_n * p_n * k_n)
|
|
}
|