AMR/man/mo_property.Rd

89 lines
2.3 KiB
R

% 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_type}
\alias{mo_gramstain}
\alias{mo_aerobic}
\alias{mo_type_nl}
\alias{mo_gramstain_nl}
\title{Property of a microorganism}
\usage{
mo_property(x, property = "fullname")
mo_family(x)
mo_genus(x)
mo_species(x)
mo_subspecies(x)
mo_fullname(x)
mo_type(x)
mo_gramstain(x)
mo_aerobic(x)
mo_type_nl(x)
mo_gramstain_nl(x)
}
\arguments{
\item{x}{a (vector of a) valid \code{\link{bactid}} or any text that can be coerced to a valid bactid with \code{\link{as.bactid}}}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"bactid"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
}
\description{
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
}
\examples{
# All properties
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_type("E. coli") # Bacteria
mo_gramstain("E. coli") # Negative rods
mo_aerobic("E. coli") # TRUE
mo_type_nl("E. coli") # Bacterie
mo_gramstain_nl("E. coli") # Negatieve staven
# Abbreviations known in the field
mo_genus("EHEC") # Escherichia
mo_species("EHEC") # coli
mo_subspecies("EHEC") # EHEC
mo_fullname("EHEC") # Escherichia coli (EHEC)
mo_genus("MRSA") # Staphylococcus
mo_species("MRSA") # aureus
mo_gramstain("MRSA") # Positive cocci
mo_genus("VISA") # Staphylococcus
mo_species("VISA") # aureus
# Known subspecies
mo_genus("doylei") # Campylobacter
mo_species("doylei") # jejuni
mo_fullname("doylei") # Campylobacter jejuni (doylei)
# Anaerobic bacteria
mo_genus("B. fragilis") # Bacteroides
mo_species("B. fragilis") # fragilis
mo_aerobic("B. fragilis") # FALSE
}
\seealso{
\code{\link{microorganisms}}
}