mirror of https://github.com/msberends/AMR.git
91 lines
6.8 KiB
R
Executable File
91 lines
6.8 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Calculate the matching score for microorganisms
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#'
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#' This helper function is used by [as.mo()] to determine the most probable match of taxonomic records, based on user input.
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#' @param x Any user input value(s)
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#' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
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#' @section Matching score for microorganisms:
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#' 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:
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#'
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#' \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}}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}
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#'
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#' where:
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#'
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#' * \eqn{x} is the user input;
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#' * \eqn{n} is a taxonomic name (genus, species, and subspecies);
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#' * \eqn{l_n}{l_n} is the length of \eqn{n};
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#' * lev is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance), which counts any insertion, deletion and substitution as 1 that is needed to change \eqn{x} into \eqn{n};
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#' * \eqn{p_n}{p_n} is the human pathogenic prevalence group of \eqn{n}, as described below;
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#' * \eqn{k_n}{p_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.
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#'
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#' 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 Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Absidia*, *Acremonium*, *Actinotignum*, *Alternaria*, *Anaerosalibacter*, *Apophysomyces*, *Arachnia*, *Aspergillus*, *Aureobacterium*, *Aureobasidium*, *Bacteroides*, *Basidiobolus*, *Beauveria*, *Blastocystis*, *Branhamella*, *Calymmatobacterium*, *Candida*, *Capnocytophaga*, *Catabacter*, *Chaetomium*, *Chryseobacterium*, *Chryseomonas*, *Chrysonilia*, *Cladophialophora*, *Cladosporium*, *Conidiobolus*, *Cryptococcus*, *Curvularia*, *Exophiala*, *Exserohilum*, *Flavobacterium*, *Fonsecaea*, *Fusarium*, *Fusobacterium*, *Hendersonula*, *Hypomyces*, *Koserella*, *Lelliottia*, *Leptosphaeria*, *Leptotrichia*, *Malassezia*, *Malbranchea*, *Mortierella*, *Mucor*, *Mycocentrospora*, *Mycoplasma*, *Nectria*, *Ochroconis*, *Oidiodendron*, *Phoma*, *Piedraia*, *Pithomyces*, *Pityrosporum*, *Prevotella*,\\*Pseudallescheria*, *Rhizomucor*, *Rhizopus*, *Rhodotorula*, *Scolecobasidium*, *Scopulariopsis*, *Scytalidium*,*Sporobolomyces*, *Stachybotrys*, *Stomatococcus*, *Treponema*, *Trichoderma*, *Trichophyton*, *Trichosporon*, *Tritirachium* or *Ureaplasma*. **Group 3** consists of all other microorganisms.
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#'
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#' 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.
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#' @export
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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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#' mo_matching_score(x = "E. coli",
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#' n = c("Escherichia coli", "Entamoeba coli"))
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mo_matching_score <- function(x, n) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list"))
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meet_criteria(n, allow_class = "character")
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x <- parse_and_convert(x)
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# no dots and other non-whitespace characters
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x <- gsub("[^a-zA-Z0-9 \\(\\)]+", "", x)
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# only keep one space
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x <- gsub(" +", " ", x)
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# n is always a taxonomically valid full name
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if (length(n) == 1) {
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n <- rep(n, length(x))
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}
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if (length(x) == 1) {
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x <- rep(x, length(n))
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}
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# length of fullname
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l_n <- nchar(n)
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lev <- double(length = length(x))
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l_n.lev <- double(length = length(x))
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for (i in seq_len(length(x))) {
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# determine Levenshtein distance, but maximise to nchar of n
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lev[i] <- utils::adist(x[i], n[i], ignore.case = FALSE, fixed = TRUE)
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# minimum of (l_n, Levenshtein distance)
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l_n.lev[i] <- min(l_n[i], as.double(lev[i]))
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}
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# human pathogenic prevalence (1 to 3), see ?as.mo
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p_n <- MO_lookup[match(n, MO_lookup$fullname), "prevalence", drop = TRUE]
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# kingdom index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
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k_n <- MO_lookup[match(n, MO_lookup$fullname), "kingdom_index", drop = TRUE]
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# matching score:
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(l_n - 0.5 * l_n.lev) / (l_n * p_n * k_n)
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}
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