mirror of https://github.com/msberends/AMR.git
225 lines
10 KiB
R
225 lines
10 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_type}
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\alias{mo_gramstain}
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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_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{Property of a microorganism}
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\usage{
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mo_name(x, language = get_locale(), ...)
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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, language = get_locale(), ...)
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mo_order(x, language = get_locale(), ...)
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mo_class(x, language = get_locale(), ...)
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mo_phylum(x, language = get_locale(), ...)
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mo_kingdom(x, language = get_locale(), ...)
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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_snomed(x, ...)
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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, language = get_locale(), ...)
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mo_synonyms(x, ...)
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mo_info(x, language = get_locale(), ...)
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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]{as.mo()}}}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{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]{as.mo()}}}
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\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
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\item{property}{one of the column names of the \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{\link{integer}} in case of \code{\link[=mo_year]{mo_year()}}
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\item A \code{\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 \code{\link{character}} in case of \code{\link[=mo_url]{mo_url()}}
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\item A \code{\link{double}} in case of \code{\link[=mo_snomed]{mo_snomed()}}
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\item A \code{\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. 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. Please 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 according to the Catalogue of Life, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. This leads to the following results:
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\itemize{
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\item \code{mo_name("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 short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \emph{"E. coli"}. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like \emph{"CoNS"} (Coagulase-Negative Staphylococci) and \emph{"GBS"} (Group B Streptococci).
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The Gram stain - \code{\link[=mo_gramstain]{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. 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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All output will be \link{translate}d 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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}
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\section{Catalogue of Life}{
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\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
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This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
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\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
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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.} \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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\item Becker K \emph{et al.} \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).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
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\item 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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\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
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}
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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") # "Enterobacterales"
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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_name("E. coli") # "Escherichia coli"
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mo_fullname("E. coli") # "Escherichia coli" - same as mo_name()
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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_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes)
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mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
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mo_rank("E. coli") # "species"
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mo_url("E. coli") # get the direct url to the online database entry
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mo_synonyms("E. coli") # get previously accepted taxonomic names
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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("VISA") # "S. aureus"
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mo_gramstain("VISA") # "Gram-positive"
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mo_genus("EHEC") # "Escherichia"
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mo_species("EHEC") # "coli"
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# known subspecies ---------------------------------------------------------
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mo_name("doylei") # "Campylobacter jejuni doylei"
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mo_genus("doylei") # "Campylobacter"
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mo_species("doylei") # "jejuni"
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mo_subspecies("doylei") # "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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\donttest{
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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 (from kingdom to subspecies)
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mo_taxonomy("E. coli")
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# get a list with the taxonomy, the authors, Gram-stain and URL to the online database
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mo_info("E. coli")
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}
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}
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\seealso{
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\link{microorganisms}
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}
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