ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid

man/mo_property.Rd

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+% 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}}
+}