AMR/man/mo_property.Rd

139 lines
5.6 KiB
R
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo_property.R
\name{mo_property}
\alias{mo_property}
\alias{mo_family}
\alias{mo_genus}
\alias{mo_species}
\alias{mo_subspecies}
\alias{mo_fullname}
\alias{mo_shortname}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_aerobic}
\title{Property of a microorganism}
\source{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870926. \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): 57195. \url{https://dx.doi.org/10.1084/jem.57.4.571}
}
\usage{
mo_family(x)
mo_genus(x)
mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_subspecies(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_fullname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_shortname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_type(x, language = NULL)
mo_gramstain(x, language = NULL)
mo_aerobic(x)
mo_property(x, property = "fullname", Becker = FALSE,
Lancefield = FALSE, language = NULL)
}
\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, i.e. \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 the systems language. 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, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
}
\value{
Character or logical (only \code{mo_aerobic})
}
\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}}.
}
\examples{
# All properties
mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # ""
mo_fullname("E. coli") # "Escherichia coli"
mo_shortname("E. coli") # "E. coli"
mo_type("E. coli") # "Bacteria"
mo_gramstain("E. coli") # "Negative rods"
mo_aerobic("E. coli") # TRUE
# Abbreviations known in the field
mo_genus("MRSA") # "Staphylococcus"
mo_species("MRSA") # "aureus"
mo_shortname("MRSA") # "S. aureus"
mo_gramstain("MRSA") # "Positive cocci"
mo_genus("VISA") # "Staphylococcus"
mo_species("VISA") # "aureus"
# Known subspecies
mo_genus("EHEC") # "Escherichia"
mo_species("EHEC") # "coli"
mo_subspecies("EHEC") # "EHEC"
mo_fullname("EHEC") # "Escherichia coli (EHEC)"
mo_shortname("EHEC") # "E. coli"
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"
# Anaerobic bacteria
mo_genus("B. fragilis") # "Bacteroides"
mo_species("B. fragilis") # "fragilis"
mo_aerobic("B. fragilis") # FALSE
# 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") # "Negative Staebchen"
mo_gramstain("E. coli", language = "nl") # "Negatieve staven"
mo_gramstain("E. coli", language = "es") # "Bacilos negativos"
mo_gramstain("Giardia", language = "pt") # "Parasitas"
mo_fullname("S. pyo",
Lancefield = TRUE,
language = "de") # "Streptococcus Gruppe A"
mo_fullname("S. pyo",
Lancefield = TRUE,
language = "nl") # "Streptococcus groep A"
}
\seealso{
\code{\link{microorganisms}}
}