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New mo algorithm, prepare for 2.0
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Dr. Matthijs Berends
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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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) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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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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#' @author Dr. Matthijs Berends
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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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#' @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}.
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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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@@ -39,17 +44,21 @@
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#' * \ifelse{html}{\out{<i>x</i> is the user input;}}{\eqn{x} is the user input;}
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#' * \ifelse{html}{\out{<i>n</i> is a taxonomic name (genus, species, and subspecies);}}{\eqn{n} is a taxonomic name (genus, species, and subspecies);}
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#' * \ifelse{html}{\out{<i>l<sub>n</sub></i> is the length of <i>n</i>;}}{l_n is the length of \eqn{n};}
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#' * \ifelse{html}{\out{<i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance function</a>, which counts any insertion, deletion and substitution as 1 that is needed to change <i>x</i> into <i>n</i>;}}{lev is the Levenshtein distance function, which counts any insertion, deletion and substitution as 1 that is needed to change \eqn{x} into \eqn{n};}
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#' * \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};}
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#' * \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;}
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#' * \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.}
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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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#' 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:
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#'
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#' **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.
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#'
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#' **Group 2** consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`.
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#'
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#' **Group 3** consists of all other microorganisms.
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#'
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#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
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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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#'
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#' Since `AMR` version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: `r vector_and(pkg_env$mo_field_abbreviations, quotes = FALSE)`.
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#' @export
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#' @inheritSection AMR Reference Data Publicly Available
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#' @examples
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@@ -68,19 +77,12 @@ mo_matching_score <- function(x, n) {
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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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# remove abbreviations known to the field
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x <- gsub(paste0(
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"(^|[^a-z0-9]+)(",
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paste0(pkg_env$mo_field_abbreviations, collapse = "|"),
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")([^a-z0-9]+|$)"
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),
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"", x,
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perl = TRUE, ignore.case = TRUE
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)
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# only keep one space
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x <- gsub(" +", " ", x)
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# force a capital letter, so this conversion will not count as a substitution
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substr(x, 1, 1) <- toupper(substr(x, 1, 1))
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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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@@ -93,12 +95,19 @@ mo_matching_score <- function(x, n) {
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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, costs = c(ins = 1, del = 1, sub = 1))
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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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lev <- unlist(Map(f = function(a, b) {
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as.double(utils::adist(a, b,
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ignore.case = FALSE,
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fixed = TRUE,
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costs = c(insertions = 1, deletions = 2, substitutions = 2),
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counts = FALSE
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))
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}, x, n, USE.NAMES = FALSE))
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l_n.lev[l_n < lev] <- l_n[l_n < lev]
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l_n.lev[lev < l_n] <- lev[lev < l_n]
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l_n.lev[lev == l_n] <- lev[lev == l_n]
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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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