AMR/man/mo_matching_score.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo_matching_score.R
\name{mo_matching_score}
\alias{mo_matching_score}
\title{Calculate the Matching Score for Microorganisms}
\usage{
mo_matching_score(x, n)
}
\arguments{
\item{x}{Any user input value(s)}

\item{n}{A full taxonomic name, that exists in \code{\link[=microorganisms]{microorganisms$fullname}}}
}
\description{
This algorithm is used by \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions to determine the most probable match of taxonomic records based on user input.
}
\note{
This algorithm was originally developed in 2018 and subsequently described in: Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}.

Later, the work of Bartlett A \emph{et al.} about bacterial pathogens infecting humans (2022, \doi{10.1099/mic.0.001269}) was incorporated, and optimalisations to the algorithm were made.
}
\section{Matching Score for Microorganisms}{

With ambiguous user input in \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions, the returned results are chosen based on their matching score using \code{\link[=mo_matching_score]{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:
\itemize{
\item \eqn{x} is the user input;
\item \eqn{n} is a taxonomic name (genus, species, and subspecies);
\item \eqn{l_n} is the length of \eqn{n};
\item \eqn{lev} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{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};
\item \eqn{p_n} is the human pathogenic prevalence group of \eqn{n}, as described below;
\item \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 1.25, Protozoa = 1.5, Chromista = 1.75, Archaea = 2, others = 3.
}

The grouping into human pathogenic prevalence \eqn{p} is based on recent work from Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:
\itemize{
\item \strong{Established}, if a taxonomic species has infected at least three persons in three or more references. These records have \code{prevalence = 1.15} in the \link{microorganisms} data set;
\item \strong{Putative}, if a taxonomic species has fewer than three known cases. These records have \code{prevalence = 1.25} in the \link{microorganisms} data set.
}

Furthermore,
\itemize{
\item Genera from the World Health Organization's (WHO) Priority Pathogen List have \code{prevalence = 1.0} in the \link{microorganisms} data set;
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.15} in the \link{microorganisms} data set;
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cyberlindnera}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
\item All other records have \code{prevalence = 2.0} in the \link{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.

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., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}

\section{Reference Data Publicly Available}{

All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}

\examples{
mo_reset_session()

as.mo("E. coli")
mo_uncertainties()

mo_matching_score(
  x = "E. coli",
  n = c("Escherichia coli", "Entamoeba coli")
)
}