mirror of https://github.com/msberends/AMR.git
297 lines
20 KiB
R
297 lines
20 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mo_property.R
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\name{mo_property}
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\alias{mo_property}
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\alias{mo_name}
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\alias{mo_fullname}
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\alias{mo_shortname}
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\alias{mo_subspecies}
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\alias{mo_species}
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\alias{mo_genus}
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\alias{mo_family}
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\alias{mo_order}
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\alias{mo_class}
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\alias{mo_phylum}
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\alias{mo_kingdom}
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\alias{mo_domain}
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\alias{mo_type}
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\alias{mo_gramstain}
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\alias{mo_is_gram_negative}
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\alias{mo_is_gram_positive}
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\alias{mo_is_yeast}
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\alias{mo_is_intrinsic_resistant}
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\alias{mo_snomed}
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\alias{mo_ref}
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\alias{mo_authors}
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\alias{mo_year}
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\alias{mo_lpsn}
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\alias{mo_rank}
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\alias{mo_taxonomy}
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\alias{mo_synonyms}
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\alias{mo_info}
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\alias{mo_url}
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\title{Get Properties of a Microorganism}
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\usage{
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mo_name(x, language = get_AMR_locale(), ...)
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mo_fullname(x, language = get_AMR_locale(), ...)
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mo_shortname(x, language = get_AMR_locale(), ...)
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mo_subspecies(x, language = get_AMR_locale(), ...)
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mo_species(x, language = get_AMR_locale(), ...)
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mo_genus(x, language = get_AMR_locale(), ...)
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mo_family(x, language = get_AMR_locale(), ...)
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mo_order(x, language = get_AMR_locale(), ...)
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mo_class(x, language = get_AMR_locale(), ...)
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mo_phylum(x, language = get_AMR_locale(), ...)
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mo_kingdom(x, language = get_AMR_locale(), ...)
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mo_domain(x, language = get_AMR_locale(), ...)
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mo_type(x, language = get_AMR_locale(), ...)
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mo_gramstain(x, language = get_AMR_locale(), ...)
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mo_is_gram_negative(x, language = get_AMR_locale(), ...)
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mo_is_gram_positive(x, language = get_AMR_locale(), ...)
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mo_is_yeast(x, language = get_AMR_locale(), ...)
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mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(), ...)
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mo_snomed(x, language = get_AMR_locale(), ...)
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mo_ref(x, language = get_AMR_locale(), ...)
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mo_authors(x, language = get_AMR_locale(), ...)
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mo_year(x, language = get_AMR_locale(), ...)
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mo_lpsn(x, language = get_AMR_locale(), ...)
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mo_rank(x, language = get_AMR_locale(), ...)
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mo_taxonomy(x, language = get_AMR_locale(), ...)
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mo_synonyms(x, language = get_AMR_locale(), ...)
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mo_info(x, language = get_AMR_locale(), ...)
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mo_url(x, open = FALSE, language = get_AMR_locale(), ...)
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mo_property(x, property = "fullname", language = get_AMR_locale(), ...)
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}
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\arguments{
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\item{x}{any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'allow_uncertain' and 'ignore_pattern'}
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\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
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\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}
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\item{property}{one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be \code{"shortname"}}
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}
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\value{
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\itemize{
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\item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}}
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\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
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\item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
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\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
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\item A \link{character} in all other cases
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}
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}
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\description{
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Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible to use microbial abbreviations, codes and names as input. See \emph{Examples}.
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}
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\details{
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All functions will return the most recently known taxonomic property \link[=microorganisms]{as included in this package}, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
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\itemize{
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\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a message about the renaming)
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\item \code{mo_ref("Escherichia blattae")} will return \code{"Burgess et al., 1973"} (with a message about the renaming)
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\item \code{mo_ref("Shimwellia blattae")} will return \code{"Priest et al., 2010"} (without a message)
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}
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The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
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Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results.
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The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
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Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
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Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
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All output \link[=translate]{will be translated} where possible.
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The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info.
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}
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\section{Matching Score for Microorganisms}{
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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:
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\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 )}}
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where:
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\itemize{
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\item \ifelse{html}{\out{<i>x</i> is the user input;}}{\eqn{x} is the user input;}
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\item \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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\item \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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\item \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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\item \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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\item \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:
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\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
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\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \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{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
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\strong{Group 3} consists of all other microorganisms.
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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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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 = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
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}
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\section{Source}{
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\enumerate{
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\item Becker K. \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
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\item Becker K. \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
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\item Becker K. \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
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\item Lancefield R.C. (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
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\item Berends M.S. \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
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\item Parte, A.C. \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
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\item GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 12 September, 2022.
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\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
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}
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}
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\section{Reference Data Publicly Available}{
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All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, 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}.
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}
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\examples{
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# taxonomic tree -----------------------------------------------------------
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mo_kingdom("Klebsiella pneumoniae")
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mo_phylum("Klebsiella pneumoniae")
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mo_class("Klebsiella pneumoniae")
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mo_order("Klebsiella pneumoniae")
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mo_family("Klebsiella pneumoniae")
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mo_genus("Klebsiella pneumoniae")
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mo_species("Klebsiella pneumoniae")
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mo_subspecies("Klebsiella pneumoniae")
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# colloquial properties ----------------------------------------------------
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mo_name("Klebsiella pneumoniae")
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mo_fullname("Klebsiella pneumoniae")
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mo_shortname("Klebsiella pneumoniae")
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# other properties ---------------------------------------------------------
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mo_gramstain("Klebsiella pneumoniae")
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mo_snomed("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_rank("Klebsiella pneumoniae")
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mo_url("Klebsiella pneumoniae")
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mo_synonyms("Klebsiella pneumoniae")
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# scientific reference -----------------------------------------------------
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mo_ref("Klebsiella pneumoniae")
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mo_authors("Klebsiella pneumoniae")
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mo_year("Klebsiella pneumoniae")
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mo_lpsn("Klebsiella pneumoniae")
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# abbreviations known in the field -----------------------------------------
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mo_genus("MRSA")
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mo_species("MRSA")
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mo_shortname("VISA")
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mo_gramstain("VISA")
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mo_genus("EHEC")
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mo_species("EHEC")
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# known subspecies ---------------------------------------------------------
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mo_name("doylei")
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mo_genus("doylei")
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mo_species("doylei")
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mo_subspecies("doylei")
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mo_fullname("K. pneu rh")
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mo_shortname("K. pneu rh")
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\donttest{
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# Becker classification, see ?as.mo ----------------------------------------
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mo_fullname("S. epi")
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mo_fullname("S. epi", Becker = TRUE)
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mo_shortname("S. epi")
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mo_shortname("S. epi", Becker = TRUE)
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# Lancefield classification, see ?as.mo ------------------------------------
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mo_fullname("S. pyo")
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mo_fullname("S. pyo", Lancefield = TRUE)
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mo_shortname("S. pyo")
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mo_shortname("S. pyo", Lancefield = TRUE)
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# language support --------------------------------------------------------
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mo_gramstain("Klebsiella pneumoniae", language = "de")
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mo_gramstain("Klebsiella pneumoniae", language = "nl")
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mo_gramstain("Klebsiella pneumoniae", language = "es")
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# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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mo_kingdom("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
|
|
mo_type("Klebsiella pneumoniae")
|
|
|
|
mo_fullname("S. pyogenes",
|
|
Lancefield = TRUE,
|
|
language = "de"
|
|
)
|
|
mo_fullname("S. pyogenes",
|
|
Lancefield = TRUE,
|
|
language = "nl"
|
|
)
|
|
|
|
|
|
# other --------------------------------------------------------------------
|
|
|
|
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
|
|
|
|
# gram stains and intrinsic resistance can be used as a filter in dplyr verbs
|
|
if (require("dplyr")) {
|
|
example_isolates \%>\%
|
|
filter(mo_is_gram_positive())
|
|
|
|
example_isolates \%>\%
|
|
filter(mo_is_intrinsic_resistant(ab = "vanco"))
|
|
}
|
|
|
|
|
|
# get a list with the complete taxonomy (from kingdom to subspecies)
|
|
mo_taxonomy("Klebsiella pneumoniae")
|
|
|
|
# get a list with the taxonomy, the authors, Gram-stain,
|
|
# SNOMED codes, and URL to the online database
|
|
mo_info("Klebsiella pneumoniae")
|
|
}
|
|
}
|
|
\seealso{
|
|
Data set \link{microorganisms}
|
|
}
|