mirror of https://github.com/msberends/AMR.git
218 lines
9.8 KiB
R
218 lines
9.8 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_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_type}
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\alias{mo_gramstain}
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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_rank}
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\alias{mo_taxonomy}
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\alias{mo_url}
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\title{Property of a microorganism}
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\usage{
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mo_fullname(x, language = get_locale(), ...)
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mo_shortname(x, language = get_locale(), ...)
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mo_subspecies(x, language = get_locale(), ...)
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mo_species(x, language = get_locale(), ...)
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mo_genus(x, language = get_locale(), ...)
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mo_family(x, ...)
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mo_order(x, ...)
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mo_class(x, ...)
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mo_phylum(x, ...)
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mo_kingdom(x, ...)
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mo_type(x, language = get_locale(), ...)
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mo_gramstain(x, language = get_locale(), ...)
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mo_ref(x, ...)
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mo_authors(x, ...)
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mo_year(x, ...)
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mo_rank(x, ...)
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mo_taxonomy(x, ...)
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mo_url(x, open = FALSE, ...)
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mo_property(x, property = "fullname", language = get_locale(), ...)
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}
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
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\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{...}{other parameters passed on to \code{\link{as.mo}}}
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\item{open}{browse the URL using \code{\link[utils]{browseURL}}}
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\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
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}
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\value{
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\itemize{
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\item{An \code{integer} in case of \code{mo_year}}
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\item{A \code{list} in case of \code{mo_taxonomy}}
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\item{A named \code{character} in case of \code{mo_url}}
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\item{A \code{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 from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
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}
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\details{
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All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
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\itemize{
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\item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
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\item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)}
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\item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
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}
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The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes (ref: \url{https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097}). These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
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The function \code{mo_url()} will return the direct URL to the species in the Catalogue of Life.
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}
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\section{Supported languages}{
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Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish), \code{"it"} (Italian), \code{"fr"} (French), and \code{"pt"} (Portuguese).
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}
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\section{Catalogue of Life}{
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\if{html}{\figure{logo_col.png}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). This data is updated annually - check the included version with \code{\link{catalogue_of_life_version}}.
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Included are:
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\itemize{
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\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
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\item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
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\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
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\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
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\item{The responsible author(s) and year of scientific publication}
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}
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The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
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The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R}.
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}
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\section{Source}{
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[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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[3] Catalogue of Life: Annual Checklist (public online database), \url{www.catalogueoflife.org}.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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## taxonomic tree
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mo_kingdom("E. coli") # "Bacteria"
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mo_phylum("E. coli") # "Proteobacteria"
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mo_class("E. coli") # "Gammaproteobacteria"
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mo_order("E. coli") # "Enterobacteriales"
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mo_family("E. coli") # "Enterobacteriaceae"
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mo_genus("E. coli") # "Escherichia"
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mo_species("E. coli") # "coli"
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mo_subspecies("E. coli") # ""
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## colloquial properties
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mo_fullname("E. coli") # "Escherichia coli"
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mo_shortname("E. coli") # "E. coli"
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## other properties
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mo_gramstain("E. coli") # "Gram negative"
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mo_type("E. coli") # "Bacteria" (equal to kingdom)
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mo_rank("E. coli") # "species"
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mo_url("E. coli") # get the direct url to the Catalogue of Life
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## scientific reference
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mo_ref("E. coli") # "Castellani et al., 1919"
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mo_authors("E. coli") # "Castellani et al."
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mo_year("E. coli") # 1919
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# Abbreviations known in the field
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mo_genus("MRSA") # "Staphylococcus"
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mo_species("MRSA") # "aureus"
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mo_shortname("MRSA") # "S. aureus"
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mo_gramstain("MRSA") # "Gram positive"
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mo_genus("VISA") # "Staphylococcus"
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mo_species("VISA") # "aureus"
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# Known subspecies
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mo_genus("doylei") # "Campylobacter"
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mo_species("doylei") # "jejuni"
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mo_fullname("doylei") # "Campylobacter jejuni doylei"
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mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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mo_shortname("K. pneu rh") # "K. pneumoniae"
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# Becker classification, see ?as.mo
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mo_fullname("S. epi") # "Staphylococcus epidermidis"
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mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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mo_shortname("S. epi") # "S. epidermidis"
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mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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# Lancefield classification, see ?as.mo
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mo_fullname("S. pyo") # "Streptococcus pyogenes"
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mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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mo_shortname("S. pyo") # "S. pyogenes"
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mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
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# language support for German, Dutch, Spanish, Portuguese, Italian and French
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mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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mo_gramstain("E. coli", language = "es") # "Gram negativo"
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# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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mo_kingdom("E. coli") # "Bacteria" on a German system
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mo_type("E. coli") # "Bakterien" on a German system
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mo_type("E. coli") # "Bacteria" on an English system
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "de") # "Streptococcus Gruppe A"
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "nl") # "Streptococcus groep A"
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# get a list with the complete taxonomy (kingdom to subspecies)
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mo_taxonomy("E. coli")
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}
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\seealso{
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\code{\link{microorganisms}}
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}
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