AMR/man/mo_property.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo_property.R
\name{mo_property}
\alias{mo_property}
\alias{mo_fullname}
\alias{mo_shortname}
\alias{mo_subspecies}
\alias{mo_species}
\alias{mo_genus}
\alias{mo_family}
\alias{mo_order}
\alias{mo_class}
\alias{mo_phylum}
\alias{mo_subkingdom}
\alias{mo_type}
\alias{mo_TSN}
\alias{mo_gramstain}
\alias{mo_taxonomy}
\title{Property of a microorganism}
\usage{
mo_fullname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)

mo_shortname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)

mo_subspecies(x, Becker = FALSE, Lancefield = FALSE, language = NULL)

mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)

mo_genus(x, language = NULL)

mo_family(x)

mo_order(x)

mo_class(x)

mo_phylum(x)

mo_subkingdom(x)

mo_type(x, language = NULL)

mo_TSN(x)

mo_gramstain(x, language = NULL)

mo_property(x, property = "fullname", Becker = FALSE,
  Lancefield = FALSE, language = NULL)

mo_taxonomy(x)
}
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}

\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].

  This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}

\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.

  This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}

\item{language}{language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}

\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
}
\value{
A \code{list} (in case of \code{mo_taxonomy}) or a \code{character} otherwise
}
\description{
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}}.
}
\section{ITIS}{

\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
}

\section{Source}{

[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}

[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}

[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
}

\examples{
# All properties
mo_subkingdom("E. coli")      # "Negibacteria"
mo_phylum("E. coli")          # "Proteobacteria"
mo_class("E. coli")           # "Gammaproteobacteria"
mo_order("E. coli")           # "Enterobacteriales"
mo_family("E. coli")          # "Enterobacteriaceae"
mo_genus("E. coli")           # "Escherichia"
mo_species("E. coli")         # "coli"
mo_subspecies("E. coli")      # NA
mo_fullname("E. coli")        # "Escherichia coli"
mo_shortname("E. coli")       # "E. coli"
mo_gramstain("E. coli")       # "Gram negative"
mo_TSN("E. coli")             # 285
mo_type("E. coli")            # "Bacteria"


# Abbreviations known in the field
mo_genus("MRSA")              # "Staphylococcus"
mo_species("MRSA")            # "aureus"
mo_shortname("MRSA")          # "S. aureus"
mo_gramstain("MRSA")          # "Gram positive"

mo_genus("VISA")              # "Staphylococcus"
mo_species("VISA")            # "aureus"


# Known subspecies
mo_genus("doylei")            # "Campylobacter"
mo_species("doylei")          # "jejuni"
mo_fullname("doylei")         # "Campylobacter jejuni doylei"

mo_fullname("K. pneu rh")     # "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh")    # "K. pneumoniae"


# Becker classification, see ?as.mo
mo_fullname("S. epi")                     # "Staphylococcus epidermidis"
mo_fullname("S. epi", Becker = TRUE)      # "Coagulase Negative Staphylococcus (CoNS)"
mo_shortname("S. epi")                    # "S. epidermidis"
mo_shortname("S. epi", Becker = TRUE)     # "CoNS"

# Lancefield classification, see ?as.mo
mo_fullname("S. pyo")                     # "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE)  # "Streptococcus group A"
mo_shortname("S. pyo")                    # "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"


# Language support for German, Dutch, Spanish and Portuguese
mo_type("E. coli", language = "de")       # "Bakterium"
mo_type("E. coli", language = "nl")       # "Bacterie"
mo_type("E. coli", language = "es")       # "Bakteria"
mo_gramstain("E. coli", language = "de")  # "Gramnegativ"
mo_gramstain("E. coli", language = "nl")  # "Gram-negatief"
mo_gramstain("E. coli", language = "es")  # "Gram negativo"

mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "de")              # "Streptococcus Gruppe A"
mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "nl")              # "Streptococcus groep A"


# Complete taxonomy up to Subkingdom, returns a list
mo_taxonomy("E. coli")
}
\seealso{
\code{\link{microorganisms}}
}